Systems and methods including a rotary valve for at least one of sample preparation or sample analysis

ABSTRACT

Systems and methods for conducting designated reactions that include a fluidic network having a sample channel, a reaction chamber, and a reservoir. The sample channel is in flow communication with a sample port. The system also includes a rotary valve that has a flow channel and is configured to rotate between first and second valve positions. The flow channel fluidically couples the reaction chamber and the sample channel when the rotary valve is in the first valve position and fluidically couples the reservoir and the reaction chamber when the rotary valve is in the second valve position. A pump assembly induces a flow of a biological sample toward the reaction chamber when the rotary valve is in the first valve position and induces a flow of a reaction component from the reservoir toward the reaction chamber when the rotary valve is in the second valve position.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is continuation application of U.S. application Ser.No. 16/818,953, filed Mar. 13, 2020, which is a divisional of U.S.Application Ser. No. 15/315,638 filed on Dec. 1, 2016, which is anational stage entry of PCT Application No. PCT/US2015/034053, filed onJun. 3, 2015, which claims priority from and the benefit of U.S.Provisional Application No. 62/008,276, filed on Jun. 5, 2014. Theentire contents of each of the aforementioned applications areincorporated herein by reference.

BACKGROUND

Embodiments of the present application relate generally to systems andmethods for generating samples for biochemical analysis and/orconducting biochemical reactions and, more particularly, to systems andmethods utilizing a rotary valve.

Various biochemical protocols involve performing a large number ofcontrolled reactions on support surfaces or within designated reactionchambers. The controlled reactions may be conducted to analyze abiological sample or to prepare the biological sample for subsequentanalysis. The analysis may identify or reveal properties of chemicalsinvolved in the reactions. For example, in an array-based, cyclicsequencing assay (e.g., sequencing-by-synthesis (SBS)), a dense array ofDNA features (e.g., template nucleic acids) are sequenced throughiterative cycles of enzymatic manipulation. After each cycle, an imagemay be captured and subsequently analyzed with other images to determinea sequence of the DNA features. In another biochemical assay, an unknownanalyte having an identifiable label (e.g., fluorescent label) may beexposed to an array of known probes that have predetermined addresseswithin the array. Observing chemical reactions that occur between theprobes and the unknown analyte may help identify or reveal properties ofthe analyte.

There has been a general demand for systems that automatically performassays, such as those described above, in which the system requires lesswork by, or involvement with, the user. Presently, most platformsrequire a user to separately prepare the biological sample prior toloading the biological sample into a system for analysis. It may bedesirable for a user to load one or more biological samples into thesystem, select an assay for execution by the system, and have resultsfrom the analysis within a predetermined period of time, such as a dayor less. At least some systems used today are not capable of executingcertain protocols, such as whole genome sequencing, that provide datahaving a sufficient level of quality and within a certain cost range.

BRIEF DESCRIPTION

In accordance with an embodiment, a system is provided that includes afluidic network having a sample channel, a reaction chamber, and areservoir. The sample channel is in flow communication with a sampleport that is configured to receive a biological sample. The system alsoincludes a pump assembly that is configured to be in flow communicationwith the fluidic network. The system also includes a rotary valve thathas a flow channel and is configured to rotate between first and secondvalve positions. The flow channel fluidically couples the reactionchamber and the sample channel when the rotary valve is in the firstvalve position and fluidically couples the reservoir and the reactionchamber when the rotary valve is in the second valve position. The pumpassembly induces a flow of the biological sample toward the reactionchamber when the rotary valve is in the first valve position and inducesa flow of a reaction component from the reservoir toward the reactionchamber when the rotary valve is in the second valve position.

In an embodiment, a method is provided that includes rotating a rotaryvalve having a flow channel to a first valve position. The flow channelis in flow communication with a reaction chamber when in the first valveposition. The method may also include flowing a biological sample from asample channel or a first reservoir through the flow channel and intothe reaction chamber when the rotary valve is in the first valveposition. The method may also include rotating the rotary valve to asecond valve position. The flow channel may fluidically couple a secondreservoir and the reaction chamber when in the second valve position.The method may also include flowing a reaction component from the secondreservoir into the reaction chamber. The reaction component interactswith the biological sample within the reaction chamber.

In an embodiment, a system is provided that includes a flow-controlsystem having a fluidic network and a pump assembly that is in flowcommunication with the fluidic network. The fluidic network includes asample channel that is configured to receive a biological sample, aplurality of reservoirs, and a reaction chamber. The system alsoincludes a rotary valve having a flow channel. The rotary valve isconfigured to rotate to different valve positions to fluidically couplethe reaction chamber to the sample channel or to one of the reservoirs.The system also includes a detection device that is configured to detectlight signals from the reaction chamber during an assay protocol. Thesystem also includes a system controller that is configured to controlthe rotary valve and the pump assembly to flow the biological samplefrom the sample channel and into the reaction chamber. The systemcontroller is also configured to control the rotary valve, the pumpassembly, and the detection device during a plurality of protocolcycles, wherein each of the protocol cycles includes: (a) rotating therotary valve to a first reservoir-valve position such that the reactionchamber is in flow communication with a first reservoir of the pluralityof reservoirs; (b) controlling the pump assembly to induce a flow of afluid from the first reservoir into the reaction chamber; (c) rotatingthe rotary valve to a second reservoir-valve position such that thereaction chamber is in flow communication with a second reservoir of theplurality of reservoirs; (d) controlling the pump assembly to induce aflow of a fluid from the second reservoir into the reaction chamber; and(e) controlling the detection device to detect the light signals fromthe reaction chamber while the fluid from the second reservoir flowsthrough the reaction chamber or after the fluid from the secondreservoir flows through the reaction chamber.

In accordance with an embodiment, a method is provided that includesproviding a microfluidic body and a rotary valve. The microfluidic bodyhas a body side and a fluidic network that includes a supply port and afeed port. The supply port opens to the body side. The rotary valve isrotatably mounted to the body side. The rotary valve has a first channelport, a second channel port, and a flow channel that extends between thefirst channel port and the second channel port. The method also includesrotating the rotary valve to a first valve position at which the firstchannel port is in flow communication with the supply port of themicrofluidic body. The method also includes flowing a biological samplethrough the first channel port and into the flow channel when the rotaryvalve is in the first valve position. The method also includes rotatingthe rotary valve to a second valve position with the biological samplewithin the flow channel such that the first channel port is sealed bythe body side. The method also includes performing a thermocyclingoperation to change a temperature of the biological sample in the flowchannel to a select temperature.

In accordance with an embodiment, a system is provided that includes amicrofluidic body having a body side and a fluidic network that includesa supply port and a feed port. The supply port opens to the body side.The system also includes a rotary valve that is rotatably mounted to thebody side. The rotary valve has a first channel port, a second channelport, and a flow channel that extends between the first and secondchannel ports. The rotary valve is configured to rotate between firstand second valve positions. The first channel port is in flowcommunication with the supply port of the microfluidic body when therotary valve is in the first valve position. The first channel port issealed by the microfluidic body when the rotary valve is in the secondvalve position. The system also includes a pump assembly that isconfigured to induce a flow of a fluid through the supply port and intothe flow channel when the rotary valve is in the first valve position.The system also includes a thermocycler that is positioned relative tothe rotary valve and configured to control a temperature experienced bythe fluid within the flow channel when the rotary valve is in the secondvalve position.

In accordance with an embodiment, a system is provided that includes amicrofluidic body having a fluidic network that has an inlet port, anoutlet port, and a sample reservoir. The system also includes a rotaryvalve that is rotatably coupled to the microfluidic body. The rotaryvalve has a first channel segment and a second channel segment. Thefirst channel segment fluidically couples the inlet port and the samplereservoir when the rotary valve is in a first valve position. The secondchannel segment fluidically couples the outlet port and the samplereservoir when the rotary valve is in the first valve position. Thesystem also includes a pump assembly configured to flow a fluid throughthe inlet port and the first channel segment into the sample reservoirwhen the rotary valve is in the first valve position. The rotary valveis configured to move to a second valve position in which the samplereservoir is sealed by the rotary valve. The system may also include athermocycler that is positioned relative to the microfluidic body toprovide thermal energy to the sample reservoir when the rotary valve isin the second valve position.

In accordance with an embodiment, a system is provided that includes amicrofluidic body having a fluidic network that has a sample reservoirand a separate assay channel. The assay channel extends between firstand second ports. The fluidic network also includes a feed port. Thesystem may also include a thermocycler that is positioned adjacent to athermal-control area of the microfluidic body. The assay channel extendsthrough the thermal-control area. The thermocycler is configured toprovide thermal energy to the thermal-control area. The system alsoincludes a rotary valve that is rotatably coupled to the microfluidicbody and configured to move between first and second valve positions.The rotary valve has a bridge channel and a separate flow channel. Thebridge channel fluidically couples the sample reservoir and the firstport of the assay channel and the flow channel fluidically couples thesecond port of the assay channel and the feed port when the rotary valveis in the first valve position. The rotary valve is configured to moveto a second valve position to seal the first and second ports of theassay channel.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic diagram of a system formed in accordance with anembodiment that is configured to conduct at least one of biochemicalanalysis or sample preparation.

FIG. 2 is a plan view of a flow-control system formed in accordance withan embodiment that may be used with the system of FIG. 1 .

FIG. 3 is a cross-section of a valving mechanism in a first state orcondition that may be used with the flow-control system of FIG. 2 .

FIG. 4 is a cross-section of a valving mechanism of FIG. 3 in a secondstate or condition.

FIG. 5 is a cross-section of a valving mechanism in a first state orcondition that may be used with the flow-control system of FIG. 2 .

FIG. 6 is a cross-section of a valving mechanism of FIG. 5 in a secondstate or condition.

FIG. 7 is a cross-section of a valving mechanism in a first state orcondition that may be used with the flow-control system of FIG. 2 .

FIG. 8 is a cross-section of a valving mechanism of FIG. 7 in a secondstate or condition.

FIG. 9 is a cross-section of a rotary valve mounted to a microfluidicbody in accordance with an embodiment.

FIG. 10 is a plan view of the microfluidic body of FIG. 9 .

FIG. 11 is a cross-section of a detection assembly that may be used todetect designated reactions from a reaction chamber.

FIG. 12 is a flowchart of a method in accordance with an embodiment.

FIG. 13 is a plan view of a rotary valve formed in accordance with anembodiment that is rotatably mounted to a microfluidic body.

FIG. 14 is a cross-section of the rotary valve of FIG. 13 that isrotatably mounted to the microfluidic body.

FIGS. 15A-15L illustrate different rotational positions of the rotaryvalve during different stages of an assay protocol.

FIG. 16 is a plan view of a rotary valve formed in accordance with anembodiment.

FIG. 17 is a plan view of the rotary valve of FIG. 16 during anamplification protocol.

FIG. 18 is a plan view of a rotary valve formed in accordance with anembodiment.

FIG. 19 is a method in accordance with an embodiment.

FIG. 20 is a perspective view of a flow-control system formed inaccordance with an embodiment that includes a rotary valve and amicrofluidic body.

FIG. 21 is a perspective view of the flow-control system of FIG. 20 whenthe rotary valve is in a designated position for an amplificationprotocol.

FIG. 22 is an isolated cross-section of the flow-control system of FIG.20 .

FIG. 23 is a schematic diagram of a system formed in accordance with anembodiment that is configured to conduct at least one of biochemicalanalysis or sample preparation.

FIG. 24 is a plan view of a flow-control system formed in accordancewith an embodiment that utilizes bridge channels.

FIG. 25 is a partially exploded perspective view of the flow-controlsystem of FIG. 24 .

FIG. 26 is a bottom perspective view of a rotary valve in accordancewith an embodiment.

FIG. 27 is a side perspective view of the rotary valve of FIG. 26 .

FIG. 28 illustrates a cross-section of the rotary valve of FIG. 26 .

FIG. 29 is an enlarged cross-section of the rotary valve of FIG. 26 .

DETAILED DESCRIPTION

Embodiments set forth herein may be used to perform designated reactionsfor sample preparation and/or biochemical analysis. As used herein, theterm “biochemical analysis” may include at least one of biologicalanalysis or chemical analysis. FIG. 1 is a schematic diagram of a system100 that is configured to conduct biochemical analysis and/or samplepreparation. The system 100 includes a base instrument 102 and aremovable cartridge 104 that is configured to separably engage the baseinstrument 102. The base instrument 102 and the removable cartridge 104may be configured to interact with each other to transport a biologicalsample to different locations within the system 100, to conductdesignated reactions that include the biological sample in order toprepare the biological sample for subsequent analysis, and, optionally,to detect one or more events with the biological sample. The events maybe indicative of a designated reaction with the biological sample. Theremovable cartridge 104 may be similar to an integrated microfluidiccartridge, such as those shown and described in U.S. Provisional PatentApplication No. 62/003,264, filed on May 27, 2014, which is incorporatedherein by reference in its entirety. Embodiments set forth herein,however, are not limited to integrated devices, but may also be used inlarger systems.

Although the following is with reference to the base instrument 102 andthe removable cartridge 104 as shown in FIG. 1 , it is understood thatthe base instrument 102 and the removable cartridge 104 illustrate onlyone exemplary embodiment of the system 100 and that other embodimentsexist. For example, the base instrument 102 and the removable cartridge104 include various components and features that, collectively, executea number of operations for preparing the biological sample and/oranalyzing the biological sample. In the illustrated embodiment, each ofthe base instrument 102 and the removable cartridge 104 are capable ofperforming certain functions. It is understood, however, that the baseinstrument 102 and the removable cartridge 104 may perform differentfunctions and/or may share such functions. For example, in theillustrated embodiment, the removable cartridge 104 is configured todetect the designated reactions using a detection assembly (e.g.,imaging device). In alternative embodiments, the base instrument 102 mayinclude the detection assembly. As another example, in the illustratedembodiment, the base instrument 102 is a “dry” instrument that does notprovide, receive, or exchange liquids with the removable cartridge 104.In alternative embodiments, the base instrument 102 may provide, forexample, reagents or other liquids to the removable cartridge 104 thatare subsequently consumed (e.g., used in designated reactions) by theremovable cartridge 104.

As used herein, the biological sample may include one or more biologicalor chemical substances, such as nucleosides, nucleic acids,polynucleotides, oligonucleotides, proteins, enzymes, polypeptides,antibodies, antigens, ligands, receptors, polysaccharides,carbohydrates, polyphosphates, nanopores, organelles, lipid layers,cells, tissues, organisms, and/or biologically active chemicalcompound(s), such as analogs or mimetics of the aforementioned species.In some instances, the biological sample may include whole blood,lymphatic fluid, serum, plasma, sweat, tear, saliva, sputum,cerebrospinal fluid, amniotic fluid, seminal fluid, vaginal excretion,serous fluid, synovial fluid, pericardial fluid, peritoneal fluid,pleural fluid, transudates, exudates, cystic fluid, bile, urine, gastricfluid, intestinal fluid, fecal samples, liquids containing single ormultiple cells, liquids containing organelles, fluidized tissues,fluidized organisms, liquids containing multi-celled organisms,biological swabs and biological washes.

In some embodiments, the biological sample may include an addedmaterial, such as water, deionized water, saline solutions, acidicsolutions, basic solutions, detergent solutions and/or pH buffers. Theadded material may also include reagents that will be used during thedesignated assay protocol to conduct the biochemical reactions. Forexample, added liquids may include material to conduct multiplepolymerase-chain-reaction (PCR) cycles with the biological sample.

It should be understood, however, that the biological sample that isanalyzed may be in a different form or state than the biological sampleloaded into the system 100. For example, the biological sample loadedinto the system 100 may include whole blood or saliva that issubsequently treated (e.g., via separation or amplification procedures)to provide prepared nucleic acids. The prepared nucleic acids may thenbe analyzed (e.g., quantified by PCR or sequenced by SBS) by the system100. Accordingly, when the term “biological sample” is used whiledescribing a first operation, such as PCR, and used again whiledescribing a subsequent second operation, such as sequencing, it isunderstood that the biological sample in the second operation may bemodified with respect to the biological sample prior to or during thefirst operation. For example, a sequencing step (e.g. SBS) may becarried out on amplicon nucleic acids that were produced from templatenucleic acids that were amplified in a prior amplification step (e.g.PCR). In this case the amplicons are copies of the templates and theamplicons are present in higher quantity compared to the quantity of thetemplates.

In some embodiments, the system 100 may automatically prepare a samplefor biochemical analysis based on a substance provided by the user(e.g., whole blood or saliva). However, in other embodiments, the system100 may analyze biological samples that are partially or preliminarilyprepared for analysis by the user. For example, the user may provide asolution including nucleic acids that were already isolated and/oramplified from whole blood.

As used herein, a “designated reaction” includes a change in at leastone of a chemical, electrical, physical, or optical property (orquality) of an analyte-of-interest. In particular embodiments, thedesignated reaction is an associative binding event (e.g., incorporationof a fluorescently labeled biomolecule with the analyte-of-interest).The designated reaction can be a dissociative binding event (e.g.,release of a fluorescently labeled biomolecule from ananalyte-of-interest). The designated reaction may be a chemicaltransformation, chemical change, or chemical interaction. The designatedreaction may also be a change in electrical properties. For example, thedesignated reaction may be a change in ion concentration within asolution. Exemplary reactions include, but are not limited to, chemicalreactions such as reduction, oxidation, addition, elimination,rearrangement, esterification, amidation, etherification, cyclization,or substitution; binding interactions in which a first chemical binds toa second chemical; dissociation reactions in which two or more chemicalsdetach from each other; fluorescence; luminescence; bioluminescence;chemiluminescence; and biological reactions, such as nucleic acidreplication, nucleic acid amplification, nucleic acid hybridization,nucleic acid ligation, phosphorylation, enzymatic catalysis, receptorbinding, or ligand binding. The designated reaction can also be additionor elimination of a proton, for example, detectable as a change in pH ofa surrounding solution or environment. An additional designated reactioncan be detecting the flow of ions across a membrane (e.g., natural orsynthetic bilayer membrane), for example as ions flow through a membranethe current is disrupted and the disruption can be detected. Fieldsensing of charged tags can also be used as can thermal sensing andother analytical sensing techniques known in the art.

In particular embodiments, the designated reaction includes theincorporation of a fluorescently-labeled molecule to an analyte. Theanalyte may be an oligonucleotide and the fluorescently-labeled moleculemay be a nucleotide. The designated reaction may be detected when anexcitation light is directed toward the oligonucleotide having thelabeled nucleotide, and the fluorophore emits a detectable fluorescentsignal. In alternative embodiments, the detected fluorescence is aresult of chemiluminescence or bioluminescence. A designated reactionmay also increase fluorescence (or Förster) resonance energy transfer(FRET), for example, by bringing a donor fluorophore in proximity to anacceptor fluorophore, decrease FRET by separating donor and acceptorfluorophores, increase fluorescence by separating a quencher from afluorophore or decrease fluorescence by co-locating a quencher andfluorophore.

As used herein, a “reaction component” includes any substance that maybe used to obtain a designated reaction. For example, reactioncomponents include reagents, catalysts such as enzymes, reactants forthe reaction, samples, products of the reaction, other biomolecules,salts, metal cofactors, chelating agents, and buffer solutions (e.g.,hydrogenation buffer). The reaction components may be delivered,individually in solutions or combined in one or more mixture, to variouslocations in a fluidic network. For instance, a reaction component maybe delivered to a reaction chamber where the biological sample isimmobilized. The reaction components may interact directly or indirectlywith the biological sample. In some embodiments, the removable cartridge104 is pre-loaded with one or more of the reaction components that arenecessary for carrying out a designated assay protocol. Preloading canoccur at one location (e.g. a manufacturing facility) prior to receiptof the cartridge 104 by a user (e.g. at a customer's facility).

In some embodiments, the base instrument 102 may be configured tointeract with one removable cartridge 104 per session. After thesession, the removable cartridge 104 may be replaced with anotherremovable cartridge 104. In other embodiments, the base instrument 102may be configured to interact with more than one removable cartridge 104per session. As used herein, the term “session” includes performing atleast one of sample preparation and/or biochemical analysis protocol.Sample preparation may include separating, isolating, modifying and/oramplifying one or more components of the biological sample so that theprepared biological sample is suitable for analysis. In someembodiments, a session may include continuous activity in which a numberof controlled reactions are conducted until (a) a designated number ofreactions have been conducted, (b) a designated number of events havebeen detected, (c) a designated period of system time has elapsed, (d)signal-to-noise has dropped to a designated threshold; (e) a targetcomponent has been identified; (f) system failure or malfunction hasbeen detected; and/or (g) one or more of the resources for conductingthe reactions has depleted. Alternatively, a session may include pausingsystem activity for a period of time (e.g., minutes, hours, days, weeks)and later completing the session until at least one of (a)-(g) occurs.

An assay protocol may include a sequence of operations for conductingthe designated reactions, detecting the designated reactions, and/oranalyzing the designated reactions. Collectively, the removablecartridge 104 and the base instrument 102 may include the componentsthat are necessary for executing the different operations. Theoperations of an assay protocol may include fluidic operations,thermal-control operations, detection operations, and/or mechanicaloperations. A fluidic operation includes controlling the flow of fluid(e.g., liquid or gas) through the system 100, which may be actuated bythe base instrument 102 and/or by the removable cartridge 104. Forexample, a fluidic operation may include controlling a pump to induceflow of the biological sample or a reaction component into a reactionchamber. A thermal-control operation may include controlling atemperature of a designated portion of the system 100. By way ofexample, a thermal-control operation may include raising or lowering atemperature of a polymerase chain reaction (PCR) zone where a liquidthat includes the biological sample is stored. A detection operation mayinclude controlling activation of a detector or monitoring activity ofthe detector to detect predetermined properties, qualities, orcharacteristics of the biological sample. As one example, the detectionoperation may include capturing images of a designated area thatincludes the biological sample to detect fluorescent emissions from thedesignated area. The detection operation may include controlling a lightsource to illuminate the biological sample or controlling a detector toobserve the biological sample. A mechanical operation may includecontrolling a movement or position of a designated component. Forexample, a mechanical operation may include controlling a motor to movea valve-control component in the base instrument 102 that operablyengages a movable valve in the removable cartridge 104. In some cases, acombination of different operations may occur concurrently. For example,the detector may capture images of the reaction chamber as the pumpcontrols the flow of fluid through the reaction chamber. In some cases,different operations directed toward different biological samples mayoccur concurrently. For instance, a first biological sample may beundergoing amplification (e.g., PCR) while a second biological samplemay be undergoing detection.

Similar or identical fluidic elements (e.g., channels, ports,reservoirs, etc.) may be labeled differently to more readily distinguishthe fluidic elements. For example, ports may be referred to as reservoirports, supply ports, network ports, feed port, etc. It is understoodthat two or more fluidic elements that are labeled differently (e.g.,reservoir channel, sample channel, flow channel, bridge channel) do notrequire that the fluidic elements be structurally different. Moreover,the claims may be amended to add such labels to more readily distinguishsuch fluidic elements in the claims.

A “liquid,” as used herein, is a substance that is relativelyincompressible and has a capacity to flow and to conform to a shape of acontainer or a channel that holds the substance. A liquid may be aqueousbased and include polar molecules exhibiting surface tension that holdsthe liquid together. A liquid may also include non-polar molecules, suchas in an oil-based or non-aqueous substance. It is understood thatreferences to a liquid in the present application may include a liquidthat was formed from the combination of two or more liquids. Forexample, separate reagent solutions may be later combined to conductdesignated reactions.

The removable cartridge 104 is configured to separably engage orremovably couple to the base instrument 102. As used herein, when theterms “separably engaged” or “removably coupled” (or the like) are usedto describe a relationship between a removable cartridge and a baseinstrument, the term is intended to mean that a connection between theremovable cartridge and the base instrument is readily separable withoutdestroying the base instrument. Accordingly, the removable cartridge maybe separably engaged to the base instrument in an electrical manner suchthat the electrical contacts of the base instrument are not destroyed.The removable cartridge may be separably engaged to the base instrumentin a mechanical manner such that features of the base instrument thathold the removable cartridge are not destroyed. The removable cartridgemay be separably engaged to the base instrument in a fluidic manner suchthat the ports of the base instrument are not destroyed. The baseinstrument is not considered to be “destroyed,” for example, if only asimple adjustment to the component (e.g., realigning) or a simplereplacement (e.g., replacing a nozzle) is required. Components (e.g.,the removable cartridge 104 and the base instrument 102) may be readilyseparable when the components can be separated from each other withoutundue effort or a significant amount of time spent in separating thecomponents. In some embodiments, the removable cartridge 104 and thebase instrument 102 may be readily separable without destroying eitherthe removable cartridge 104 or the base instrument 102.

In some embodiments, the removable cartridge 104 may be permanentlymodified or partially damaged during a session with the base instrument102. For instance, containers holding liquids may include foil coversthat are pierced to permit the liquid to flow through the system 100. Insuch embodiments, the foil covers may be damaged such that it may benecessary to replace the damaged container with another container. Inparticular embodiments, the removable cartridge 104 is a disposablecartridge such that the removable cartridge 104 may be replaced andoptionally disposed after a single use.

In other embodiments, the removable cartridge 104 may be used for morethan one session while engaged with the base instrument 102 and/or maybe removed from the base instrument 102, reloaded with reagents, andre-engaged to the base instrument 102 to conduct additional designatedreactions. Accordingly, the removable cartridge 104 may be refurbishedin some cases such that the same removable cartridge 104 may be usedwith different consumables (e.g., reaction components and biologicalsamples). Refurbishing can be carried out at a manufacturing facilityafter the cartridge has been removed from a base instrument located at acustomer's facility.

As shown in FIG. 1 , the removable cartridge 104 includes a fluidicnetwork 106 that may hold and direct fluids (e.g., liquids or gases)therethrough. The fluidic network 106 includes a plurality ofinterconnected fluidic elements that are capable of storing a fluidand/or permitting a fluid to flow therethrough. Non-limiting examples offluidic elements include channels, ports of the channels, cavities,storage modules, reservoirs of the storage modules, reaction chambers,waste reservoirs, detection chambers, multipurpose chambers for reactionand detection, and the like. The fluidic elements may be fluidicallycoupled to one another in a designated manner so that the system 100 iscapable of performing sample preparation and/or analysis.

As used herein, the term “fluidically coupled” (or like term) refers totwo spatial regions being connected together such that a liquid or gasmay be directed between the two spatial regions. In some cases, thefluidic coupling permits a fluid to be directed back and forth betweenthe two spatial regions. In other cases, the fluidic coupling isuni-directional such that there is only one direction of flow betweenthe two spatial regions. For example, an assay reservoir may befluidically coupled with a channel such that a liquid may be transportedinto the channel from the assay reservoir. However, in some embodiments,it may not be possible to direct the fluid in the channel back to theassay reservoir. In particular embodiments, the fluidic network 106 isconfigured to receive a biological sample and direct the biologicalsample through sample preparation and/or sample analysis. The fluidicnetwork 106 may direct the biological sample and other reactioncomponents to a waste reservoir.

One or more embodiments may include retaining the biological sample(e.g., template nucleic acid) at a designated location where thebiological sample is analyzed. As used herein, the term “retained,” whenused with respect to a biological sample, includes substantiallyattaching the biological sample to a surface or confining the biologicalsample within a designated space. As used herein, the term“immobilized,” when used with respect to a biological sample, includessubstantially attaching the biological sample to a surface in or on asolid support. Immobilization may include attaching the biologicalsample at a molecular level to the surface. For example, a biologicalsample may be immobilized to a surface of a substrate using adsorptiontechniques including non-covalent interactions (e.g., electrostaticforces, van der Waals, and dehydration of hydrophobic interfaces) andcovalent binding techniques where functional groups or linkersfacilitate attaching the biological sample to the surface. Immobilizinga biological sample to a surface of a substrate may be based upon theproperties of the surface of the substrate, the liquid medium carryingthe biological sample, and the properties of the biological sampleitself. In some cases, a substrate surface may be functionalized (e.g.,chemically or physically modified) to facilitate immobilizing thebiological sample to the substrate surface. The substrate surface may befirst modified to have functional groups bound to the surface. Thefunctional groups may then bind to the biological sample to immobilizethe biological sample thereon. In some cases, a biological sample can beimmobilized to a surface via a gel, for example, as described in USPatent Publ. Nos. 2011/0059865 A1 and 2014/0079923 A1, each of which isincorporated herein by reference in its entirety.

In some embodiments, nucleic acids can be immobilized to a surface andamplified using bridge amplification. Useful bridge amplificationmethods are described, for example, in U.S. Pat. No. 5,641,658; WO07/010251, U.S. Pat. No. 6,090,592; U.S. Patent Publ. No. 2002/0055100A1; U.S. Pat. No. 7,115,400; U.S. Patent Publ. No. 2004/0096853 A1; U.S.Patent Publ. No. 2004/0002090 A1; U.S. Patent Publ. No. 2007/0128624 A1;and U.S. Patent Publ. No. 2008/0009420 A1, each of which is incorporatedherein in its entirety. Another useful method for amplifying nucleicacids on a surface is rolling circle amplification (RCA), for example,using methods set forth in further detail below. In some embodiments,the nucleic acids can be attached to a surface and amplified using oneor more primer pairs. For example, one of the primers can be in solutionand the other primer can be immobilized on the surface (e.g.,5′-attached). By way of example, a nucleic acid molecule can hybridizeto one of the primers on the surface followed by extension of theimmobilized primer to produce a first copy of the nucleic acid. Theprimer in solution then hybridizes to the first copy of the nucleic acidwhich can be extended using the first copy of the nucleic acid as atemplate. Optionally, after the first copy of the nucleic acid isproduced, the original nucleic acid molecule can hybridize to a secondimmobilized primer on the surface and can be extended at the same timeor after the primer in solution is extended. In any embodiment, repeatedrounds of extension (e.g., amplification) using the immobilized primerand primer in solution provide multiple copies of the nucleic acid. Insome embodiments, the biological sample may be confined within apredetermined space with reaction components that are configured to beused during amplification of the biological sample (e.g., PCR).

One or more embodiments set forth herein may be configured to execute anassay protocol that is or includes an amplification (or PCR) protocol.During the amplification protocol, a temperature of the biologicalsample within a reservoir or channel may be changed in order to amplifythe biological sample (e.g., DNA of the biological sample). By way ofexample, the biological sample may experience (1) a pre-heating stage ofabout 95° C. for about 75 seconds; (2) a denaturing stage of about 95°C. for about 15 seconds; (3) an annealing-extension stage of about ofabout 59° C. for about 45 seconds; and (4) a temperature holding stageof about 72° C. for about 60 seconds. Embodiments may execute multipleamplification cycles. It is noted that the above cycle describes onlyone particular embodiment and that alternative embodiments may includemodifications to the amplification protocol.

The methods and systems set forth herein can use arrays having featuresat any of a variety of densities including, for example, at least about10 features/cm², 100 features/cm², 500 features/cm², 1,000 features/cm²,5,000 features/cm², 10,000 features/cm², 50,000 features/cm², 100,000features/cm², 1,000,000 features/cm², features/cm², or higher. Themethods and apparatus set forth herein can include detection componentsor devices having a resolution that is at least sufficient to resolveindividual features at one or more of these exemplified densities.

In the illustrated embodiment, the removable cartridge 104 includes acartridge housing 110 having a plurality of housing sides 111-114. Thehousing sides 111-114 include non-mating sides 111-113 and a mating side114. The mating side 114 is configured to engage the base instrument102. In the illustrated embodiment, the cartridge housing 110 forms asubstantially unitary structure. In alternative embodiments, thecartridge housing 110 may be constructed by one or more sub-componentsthat are combined by a user of the system 100. The sub-components may becombined before the removable cartridge 104 is separably engaged to thebase instrument 102 or after one of the sub-components is separablyengaged to the base instrument 102. For example, a storage module 150may be held by a first sub-housing (not shown) and a remainder of theremovable cartridge 104 (e.g., fluidic network and imaging device) mayinclude a second sub-housing (not shown). The first and secondsub-housings may be combined to form the cartridge housing 110.

The fluidic network 106 is held by the cartridge housing 110 andincludes a plurality of sample ports 116 that open to the non-matingside 112. In alternative embodiments, the sample ports 116 may belocated along the non-mating sides 111 or 113 or may be located alongthe mating side 114. Each of the sample ports 116 is configured toreceive a biological sample. By way of example only, the biologicalsample may be whole blood or saliva. In some embodiments, the biologicalsample may be nucleic acids and other materials (e.g., reagents,buffers, etc.) for conducting PCR. Although three sample ports 116 areshown in FIG. 1 , embodiments may include only one sample port, twosample ports, or more than three sample ports.

The fluidic network 106 also includes a fluidic-coupling port 118 thatopens to the mating side 114 and is exposed to an exterior of thecartridge housing 110. The fluidic-coupling port 118 is configured tofluidically couple to a system pump 119 of the base instrument 102. Thefluidic-coupling port 118 is in flow communication with a pump channel133 that is part of the fluidic network 106. During operation of thesystem 100, the system pump 119 is configured to provide a negativepressure for inducing a flow of fluid through the pump channel 133 andthrough a remainder of the fluidic network 106. For example, the systempump 119 may induce flow of the biological sample from the sample port116 to a sample-preparation region 132, wherein the biological samplemay be prepared for subsequent analysis. The system pump 119 may induceflow of the biological sample from the sample-preparation region 132 toa reaction chamber 126, wherein detection operations are conducted toobtain data (e.g., imaging data) of the biological sample. The systempump 119 may also induce flow of fluid from reservoirs 151, 152 of astorage module 150 to the reaction chamber 126. After the detectionoperations are conducted, the system pump 119 may induce flow of thefluid into a waste reservoir 128.

In addition to the fluidic network 106, the removable cartridge 104 mayinclude one or more mechanical interfaces 117 that may be controlled bythe base instrument 102. For example, the removable cartridge 104 mayinclude a valve assembly 120 having a plurality of flow-control valves121-123 that are operably coupled to the fluidic network 106. Each ofthe flow-control valves 121-123 may represent a mechanical interface 117that is controlled by the base instrument 102. For instance, theflow-control valves 121-123 may be selectively activated or controlledby the base instrument 102, in conjunction with selective activation ofthe system pump 119, to control a flow of fluid within the fluidicnetwork 106.

For example, in the illustrated embodiment, the fluidic network 106includes a sample channel 131 that is immediately downstream from and inflow communication with the sample ports 116. Only a single samplechannel 131 is shown in FIG. 1 , but alternative embodiments may includemultiple sample channels 131. The sample channel 131 may include thesample-preparation region 132. The valve assembly 120 includes a pair ofchannel valves 121, 122, which may also be referred to as flow-controlvalves. The channel valves 121, 122 may be selectively activated by thebase instrument 102 to impede or block flow of the fluid through thesample channel 131. In particular embodiments, the channel valves 121,122 may be activated to form a seal that retains a designated volume ofliquid within the sample-preparation region 132 of the sample channel131. The designated volume within the sample-preparation region 132 mayinclude the biological sample.

The valve assembly 120 may also include a movable valve 123. The movablevalve 123 has a valve body 138 that may include at least one flowchannel 140 that extends between corresponding ports. The valve body 138is capable of moving between different positions to align the ports withcorresponding ports of the fluidic network 106. For example, a positionof the movable valve 123 may determine the type of fluid that flows intothe reaction chamber 126. In a first position, the movable valve 123 mayalign with a corresponding port of the sample channel 131 to provide thebiological sample to the reaction chamber 126. In a second position, themovable valve 123 may align with one or more corresponding ports ofreservoir channels 161, 162 that are in flow communication with thereservoirs 151, 152, respectively, of the storage module 150. Eachreservoir 151, 152 is configured to store a reaction component that maybe used to conduct the designated reactions. The reservoir channels 161,162 are located downstream from and in flow communication with thereservoirs 151, 152, respectively. In some embodiments, the movablevalve 123 may move, separately, to different positions to align with thecorresponding ports of the reservoir channels.

In the illustrated embodiment, the movable valve 123 is a rotary valve(or rotatable valve) that is configured to rotate about an axis 142. Themovable valve 123 may be similar to the rotary valve 216 (shown FIG. 2). However, it should be understood that alternative embodiments mayinclude movable valves that do not rotate to different positions. Insuch embodiments, the movable valve may slide in one or more lineardirections to align the corresponding ports. Rotary valves andlinear-movement valves set forth herein may be similar to theapparatuses described in International Application No.PCT/US2013/032309, filed on Mar. 15, 2013, which is incorporated hereinby reference in its entirety.

In some embodiments, the biological sample is illuminated by a lightsource 158 of the base instrument 102. Alternatively, the light source158 may be incorporated with the removable cartridge 104. For example,the biological sample may include one or more fluorophores that providelight emissions when excited by a light having a suitable wavelength. Inthe illustrated embodiment, the removable cartridge 104 has an opticalpath 154. The optical path 154 is configured to permit illuminationlight 156 from the light source 158 of the base instrument 102 to beincident on the biological sample within the reaction chamber 126. Thus,the reaction chamber may have one or more optically transparent sides orwindows. The optical path 154 may include one or more optical elements,such as lenses, reflectors, fiber-optic lines, and the like, thatactively direct the illumination light 156 to the reaction chamber 126.In an exemplary embodiment, the light source 158 may be a light-emittingdiode (LED). However, in alternative embodiments, the light source 158may include other types of light-generating devices, such as lasers orlamps.

In some embodiments, the detection assembly 108 includes an imagingdetector 109 and the reaction chamber 126. The imaging detector 109 isconfigured to detect designated reactions within the reaction chamber126. In some embodiments, the imaging detector 109 may be positionedrelative to the reaction chamber 126 to detect light signals (e.g.,absorbance, reflection/refraction, or light emissions) from the reactionchamber 126. The imaging detector 109 may include one or more imagingdevices, such as a charge-coupled device (CCD) camera orcomplementary-metal-oxide semiconductor (CMOS) imager. In someembodiments, the imaging detector 109 may detect light signals that areemitted from chemilluminescence. Yet still in other embodiments, thedetection assembly 108 may not be limited to imaging applications. Forexample, the detection assembly 108 may be one or more electrodes thatdetect an electrical property of a liquid.

As set forth herein, the base instrument 102 is configured to operablyengage the removable cartridge 104 and control various operations withinthe removable cartridge 104 to conduct the designated reactions and/orobtain data of the biological sample. To this end, the mating side 114is configured to permit or allow the base instrument 102 to controloperation of one or more components of the removable cartridge 104. Forexample, the mating side 114 may include a plurality of access openings171-173 that permit the valves 121-123 to be controlled by the baseinstrument 102. The mating side 114 may also include an access opening174 that is configured to receive a thermocycler 186 (e.g., thermal orheat-transfer block) of the base instrument 102. In the illustratedembodiment, the thermocycler 186 is a thermal block. The access opening174 extends along the sample channel 131. As shown, the access openings171-174 open to the mating side 114.

In some embodiments, the fluidic network 106 and the valve assembly 123may constitute a flow-control system 164. The flow-control system 164may include the components that cooperate to control the flow of one ormore fluids through the system 100 or, more specifically, the removablecartridge 104 in order to execute one or more designated operations. Theflow-control system 164 may include additional components, such as thesystem pump 119, in other embodiments. The flow-control system 164 maybe similar or identical to the flow-control system 200 (shown in FIG. 2).

The base instrument 102 has a control side 198 configured to separablyengage the mating side 114 of the removable cartridge 104. The matingside 114 of the removable cartridge 104 and the control side 198 of thebase instrument 102 may collectively define a system interface 195. Thesystem interface 195 represents a common boundary between the removablecartridge 104 and the base instrument 102 through which the baseinstrument 102 and the removable cartridge 104 are operably engaged.More specifically, the base instrument 102 and the removable cartridge104 are operably engaged along the system interface 195 such that thebase instrument 102 may control various features of the removablecartridge 104 through the mating side 114. For instance, the baseinstrument 102 may have one or more controllable components that controlcorresponding components of the removable cartridge 104.

In some embodiments, the base instrument 102 and the removable cartridge104 are operably engaged such that the base instrument 102 and theremovable cartridge 104 are secured to each other at the systeminterface 195 with at least one of an electric coupling, thermalcoupling, optical coupling, valve coupling, or fluidic couplingestablished through the system interface 195. In the illustratedembodiment, the base instrument 102 and the removable cartridge 104 areconfigured to have an electric coupling, a thermal coupling, a valvecoupling, and an optical coupling. More specifically, the baseinstrument 102 and the removable cartridge 104 may communicate dataand/or electrical power through the electric coupling. The baseinstrument 102 and the removable cartridge 104 may convey thermal energyto and/or from each other through the thermal coupling, and the baseinstrument 102 and the removable cartridge 104 may communicate lightsignals (e.g., the illumination light) through the optical coupling.

In the illustrated embodiment, the system interface 195 is asingle-sided interface 195. For example, the control side 198 and thehousing side 114 are generally planar and face in opposite directions.The system interface 195 is single-sided such that that the removablecartridge 104 and the base instrument 102 are operably coupled to eachother only through the mating side 114 and the control side 198. Inalternative embodiments, the system interface may be a multi-sidedinterface. For example, at least 2, 3, 4, or 5 sides of a removablecartridge may be mating sides that are configured to couple with a baseinstrument. The multiple sides may be planar and may be arrangedorthogonally or opposite each other (e.g. surrounding all or part of arectangular volume).

To control operations of the removable cartridge 104, the baseinstrument 102 may include valve actuators 181-183 that are configuredto operably engage the flow-control valves 121-123, a thermocycler 186that is configured to provide and/or remove thermal energy from thesample-preparation region 132, and a contact array 188 of electricalcontacts. The base instrument 102 may also include the light source 158positioned along the control side 198. The base instrument 102 may alsoinclude the system pump 119 having a control port 199 positioned alongthe control side 198.

The system 100 may also include a locking mechanism 176. In theillustrated embodiment, the locking mechanism 176 includes a rotatablelatch 177 that is configured to engage a latch-engaging element 178 ofthe removable cartridge 104. Alternatively, the removable cartridge 104may include the rotatable latch 177 and the base instrument 102 mayinclude the latch-engaging element 178. When the removable cartridge 104is mounted to the base instrument 102, the latch 177 may be rotated andengage the latching-engaging element 178. A camming effect generated bythe locking mechanism 176 may urge or drive the removable cartridge 104toward the base instrument 102 to secure the removable cartridge 104thereto.

The base instrument 102 may include a user interface 125 that isconfigured to receive user inputs for conducting a designated assayprotocol and/or configured to communicate information to the userregarding the assay. The user interface 125 may be incorporated with thebase instrument 102. For example, the user interface 125 may include atouchscreen that is attached to a housing of the base instrument 102 andconfigured to identify a touch from the user and a location of the touchrelative to information displayed on the touchscreen. Alternatively, theuser interface 125 may be located remotely with respect to the baseinstrument 102.

The base instrument 102 may also include a system controller 180 that isconfigured to control operation of at least one of the valve actuators181-183, the thermocycler 186, the contact array 188, the light source158, or the system pump 119. The system controller 180 is illustratedconceptually as a collection of circuitry modules, but may beimplemented utilizing any combination of dedicated hardware boards,DSPs, processors, etc. Alternatively, the system controller 180 may beimplemented utilizing an off-the-shelf PC with a single processor ormultiple processors, with the functional operations distributed betweenthe processors. As a further option, the circuitry modules describedbelow may be implemented utilizing a hybrid configuration in whichcertain modular functions are performed utilizing dedicated hardware,while the remaining modular functions are performed utilizing anoff-the-shelf PC and the like.

The system controller 180 may include a plurality of circuitry modules190-193 that are configured to control operation of certain componentsof the base instrument 102 and/or the removable cartridge 104. Forinstance, the circuitry module 190 may be a flow-control module 190 thatis configured to control flow of fluids through the fluidic network 106.The flow-control module 190 may be operably coupled to the valveactuators 181-183 and the system pump 119. The flow-control module 190may selectively activate the valve actuators 181-183 and the system pump119 to induce flow of fluid through one or more paths and/or to blockflow of fluid through one or more paths.

By way of example only, the valve actuator 183 may rotatably engage themovable valve 123. The valve actuator 183 may include a rotating motor189 that is configured to drive (e.g., rotate) the valve actuator 183.The flow-control module 190 may activate the valve actuator 183 to movethe movable valve 123 to a first rotational position. With the movablevalve 123 in the first rotational position, the flow-control module 190may activate the system pump 119 thereby drawing the biological samplefrom the sample-preparation region 132 and into the reaction chamber126. The flow-control module 190 may then activate the valve actuator183 to move the movable valve 123 to a second rotational position. Withthe movable valve 123 in the second rotational position, theflow-control module 190 may activate the system pump 119 thereby drawingone or more of the reaction components from the correspondingreservoir(s) and into the reaction chamber 126. In some embodiments, thesystem pump 119 may be configured to provide positive pressure such thatthe fluid is actively pumped in an opposite direction. Such operationsmay be used to add multiple liquids into a common reservoir therebymixing the liquids within the reservoir. Accordingly, thefluidic-coupling port 118 may permit fluid (e.g., gas) to exit thecartridge housing 110 or may receive fluid into the cartridge housing110.

The system controller 180 may also include a thermal-control module 191.The thermal-control module 191 may control the thermocycler 186 toprovide and/or remove thermal energy from the sample-preparation region132. In one particular example, the thermocycler 186 may increase and/ordecrease a temperature that is experienced by the biological samplewithin the sample channel 131 in accordance with a PCR protocol.Although not shown, the system 100 may include additional thermaldevices that are positioned adjacent to the sample-preparation region132.

The system controller 180 may also include a detection module 192 thatis configured to control the detection assembly 108 to obtain dataregarding the biological sample. The detection module 192 may controloperation of the detection assembly 108 through the contact array 188.For example, the detection assembly 108 may be communicatively engagedto a contact array 194 of electrical contacts 196 along the mating side114. In some embodiment, the electrical contacts 196 may be flexiblecontacts (e.g., pogo contacts or contact beams) that are capable ofrepositioning to and from the mating side 114. The electrical contacts196 are exposed to an exterior of the cartridge housing and areelectrically coupled to the detection assembly 108. The electricalcontacts 196 may be referenced as input/output (I/O) contacts. When thebase instrument 102 and the removable cartridge 104 are operablyengaged, the detection module 192 may control the detection assembly 108to obtain data at predetermined times or for predetermined time periods.By way of example, the detection module 192 may control the detectionassembly 108 to capture an image of the reaction chamber 126 when thebiological sample has a fluorophore attached thereto. A number of imagesmay be obtained.

Optionally, the system controller 180 includes an analysis module 193that is configured to analyze the data to provide at least partialresults to a user of the system 100. For example, the analysis module193 may analyze the imaging data provided by the imaging detector 109.The analysis may include identifying a sequence of nucleic acids of thebiological sample.

The system controller 180 and/or the circuitry modules 190-193 mayinclude one or more logic-based devices, including one or moremicrocontrollers, processors, reduced instruction set computers (RISC),application specific integrated circuits (ASICs), field programmablegate array (FPGAs), logic circuits, and any other circuitry capable ofexecuting functions described herein. In an exemplary embodiment, thesystem controller 180 and/or the circuitry modules 190-193 execute a setof instructions that are stored therein in order to perform one or moreassay protocols. Storage elements may be in the form of informationsources or physical memory elements within the base instrument 102and/or the removable cartridge 104. The protocols performed by the assaysystem 100 may be to carry out, for example, quantitative analysis ofDNA or RNA, protein analysis, DNA sequencing (e.g.,sequencing-by-synthesis (SBS)), sample preparation, and/or preparationof fragment libraries for sequencing.

The set of instructions may include various commands that instruct thesystem 100 to perform specific operations such as the methods andprocesses of the various embodiments described herein. The set ofinstructions may be in the form of a software program. As used herein,the terms “software” and “firmware” are interchangeable, and include anycomputer program stored in memory for execution by a computer, includingRAM memory, ROM memory, EPROM memory, EEPROM memory, and non-volatileRAM (NVRAM) memory. The above memory types are exemplary only, and arethus not limiting as to the types of memory usable for storage of acomputer program.

The software may be in various forms such as system software orapplication software. Further, the software may be in the form of acollection of separate programs, or a program module within a largerprogram or a portion of a program module. The software also may includemodular programming in the form of object-oriented programming. Afterobtaining the detection data, the detection data may be automaticallyprocessed by the system 100, processed in response to user inputs, orprocessed in response to a request made by another processing machine(e.g., a remote request through a communication link).

The system controller 180 may be connected to the other components orsub-systems of the system 100 via communication links, which may behardwired or wireless. The system controller 180 may also becommunicatively connected to off-site systems or servers. The systemcontroller 180 may receive user inputs or commands, from a userinterface (not shown). The user interface may include a keyboard, mouse,a touch-screen panel, and/or a voice recognition system, and the like.

The system controller 180 may serve to provide processing capabilities,such as storing, interpreting, and/or executing software instructions,as well as controlling the overall operation of the system 100. Thesystem controller 180 may be configured and programmed to control dataand/or power aspects of the various components. Although the systemcontroller 180 is represented as a single structure in FIG. 1 , it isunderstood that the system controller 180 may include multiple separatecomponents (e.g., processors) that are distributed throughout the system100 at different locations. In some embodiments, one or more componentsmay be integrated with a base instrument and one or more components maybe located remotely with respect to the base instrument.

FIG. 2 is a plan view of a flow-control system 200 formed in accordancewith an embodiment. The flow-control system 200 may be part of a system(not shown) for sample preparation and/or sample analysis, such as thesystem 100 (shown in FIG. 1 ). In some embodiments, the flow-controlsystem 200 is entirely within an integrated device, such as theremovable cartridge 104 (FIG. 1 ). In other embodiments, however, theflow-control system 200 may be part of a standard system (e.g., desktopsystem). In FIG. 2 , components of the flow-control system 200 arelocated within a localized area. In other embodiments, the components ofthe flow-control system 200 may be separated from each other anddistributed in different areas.

In the illustrated embodiment, the flow-control system 200 includes afluidic network 202 that is configured to have one or more fluids (e.g.,gas or liquid) flow therethrough. The fluidic network 202 includes anarrangement of interconnected fluidic elements. The fluidic elements maybe configured to direct fluid to designated regions within the fluidicnetwork 202 where, for example, the fluid may be subjected topredetermined conditions and/or undergo designated reactions. Thefluidic elements may be selectively interconnected by one or more valvessuch that one or more fluidic elements may be disconnected with respectto one or more other fluidic elements during operation.

In the illustrated embodiment, the fluidic network 202 includes sampleports 204A-204D and sample channels 206A-206D that are in flowcommunication with the sample ports 204A-204D, respectively. The samplechannels 206A-206D extend from the corresponding sample ports 204A-204Dto a common junction or intersection 209. The fluidic network 202 alsoincludes a combined sample channel 208 that extends from the junction209 to a supply port 210 (shown in FIG. 9 ). A rotary valve 216 islocated over the supply port 210.

The fluidic network 202 also includes a feed port 226 (shown in FIG. 9 )and a feed channel 224 that extends from the feed port 226. The feedchannel 224 extends between the feed port 226 and a flow cell 320 of thefluidic network 202. The flow cell 320 includes an inlet port 322, anoutlet port 324, and a reaction chamber 326 extending therebetween.During operation, the fluid may flow from the feed channel 224 throughthe inlet port 322 and exit the reaction chamber 326 through the outletport 324. After exiting the reaction chamber 326, the fluid may flow toa waste reservoir 330 of the fluidic network 202. The waste reservoir330 is represented by a small box in FIG. 2 , but it should beunderstood that the volume of the waste reservoir 330 may be largerthan, for example, the reservoirs 240-244.

While the fluid flows through the reaction chamber 326, the fluid mayinteract with existing material (e.g., analytes) within the reactionchamber 326. Designated reactions may be detected within the reactionchamber 326. For example, a detection assembly (not shown) may bepositioned adjacent to the reaction chamber 326 and detect light signalsfrom the reaction chamber 326.

In the illustrated embodiment, the sample ports 204A-204D open to a bodyside or surface 214 of the microfluidic body 212 such that the sampleports 204A-204D are exposed to an exterior of the microfluidic body 212.The sample channels 206A-206D and the combined sample channel 208 extendthrough (e.g., within) the microfluidic body 212. The supply port 210may open to the body side 214. Alternatively, the supply port 210 mayopen to an underside (not shown) or a lateral side of the microfluidicbody 212. Accordingly, the sample channels 206A-206D are in flowcommunication with a single port, such as the supply port 210. Inalternative embodiments, however, the sample channels 206A-206D may bein flow communication with separate supply ports that open to the bodyside 214. In such alternative embodiments, each sample channel mayextend between a respective sample port and a respective supply port.

In the illustrated embodiment, the fluidic network 202 also includes aplurality of reservoir channels 220. Each of the reservoir channels 220is fluidically interposed between a reservoir port 222 (shown in FIG. 10) and a reservoir 240. The reservoir ports 222 open to the body side214. Similar to the supply port 210, the reservoir ports 222 may becovered by the rotary valve 216. Optionally, the fluidic network 202 mayinclude a reservoir channel 228 that is fluidically interposed betweenthe common sample channel 208 and a reservoir 230.

In the illustrated embodiment, the flow-control system 200 includes amicrofluidic body 212. The microfluidic body 212 may be a physicalstructure that defines the fluidic elements of the fluidic network 202.For example, the microfluidic body 212 may include stacked PCB layers inwhich one or more of the layers are etched or shaped to form one or moreof the channels (e.g., the sample channels 206A-206D, the common samplechannel 208, the reservoir channels 220, 228, and the feed channel 224)and one or more of the ports (e.g., the sample ports 204A-204D, thereservoir ports 222, the supply port 210, and the feed port 226) of thefluidic network 202. The flow cell 320 may be secured to themicrofluidic body 212. Such microfluidic bodies are illustrated anddescribed in U.S. Provisional Application No. 62/003,264 and U.S.Provisional Application No. 61/951,462. Each of these provisionalapplications is incorporated herein by reference in its entirety.Alternatively or in addition to PCB layers, other materials may be used,such as glass or plastic. In alternative embodiments, the microfluidicbody 212 may be collectively formed from multiple body components. Insome cases, the fluidic network 202 is at least partially formed bytubing.

The rotary valve 216 is configured to rotate about an axis 299 todifferent valve positions (e.g., rotational positions) to fluidicallycouple different channels of the fluidic network 202. The rotary valve216 may be slidably coupled to the body side 214 and may be positionedto cover a number of ports that open to the body side 214, such as thereservoir ports 222, the supply port 210, and the feed port 226. Therotary valve 216 includes at least one flow channel 218 (shown in FIG. 9) that is configured to fluidically connect discrete channels. Forexample, when the rotary valve 216 is in a first valve position, theflow channel 218 may fluidically connect the sample channel 208 to thefeed channel 224. When the rotary valve 216 is in a second rotationalposition, the flow channel 218 may fluidically connect one or thereservoir channels 220 to the feed channel 224.

Each of the sample ports 204A-204D is configured to receive acorresponding biological sample. For instance, a user of theflow-control system 200, such as a technician or lab worker, may load(e.g., pipette) a biological sample into one or more of the sample ports204A-204D. The biological samples may be for the same individual (e.g.,human) or may be for multiple different individuals from a population.It should be understood that the biological sample may be from otherspecies, such as animals, plants, bacteria, or fungus. In theillustrated embodiment, the sample ports 204A-204D are configured to beaccessed from an exterior of the flow-control system 200. In alternativeembodiments, the sample ports 204A-204D may be part of a larger fluidicnetwork such that the biological samples are delivered to the sampleports 204A-204D through the larger fluidic network.

As shown in FIG. 2 , each of the sample channels 206A-206D may include asample-preparation region 232. In the illustrated embodiment, the samplechannels 206A-206D have corresponding wavy or serpentine paths along thecorresponding sample-preparation region 232. The wavy or serpentinepaths may allow a greater volume of the biological sample to existwithin a thermal-control area 234. In alternative embodiments, thesample-preparation region 232 may have different dimensions than otherportions of the corresponding sample channel. For example, thesample-preparation region 232 may form a wide chamber or a well with anincreased depth.

In the sample-preparation region 232, the biological sample may undergoa process to prepare the biological sample for subsequent reactionsand/or analysis. For example, the biological sample may experience achange in pressure and/or temperature. Alternatively or in addition to,the biological sample may be mixed with one or more reaction componentswithin the sample-preparation region 232. In some embodiments, theflow-control system 200 may include a thermal-control strip or band 236(indicated by a dashed line) that extends along the thermal-control area234 that is adjacent to the sample-preparation regions 232 of the samplechannels 206A-206D. In some embodiments, the thermal-control strip 236may be a flexible PCB heater, such as the flexible PCB heater describedin U.S. Provisional Application No. 61/951,462, which is incorporated byreference in its entirety. The flexible PCB heater may extend along thethermal-control area 234 and have conductive traces therein thatgenerate heat when a current is permitted to flow therethrough.

The thermal-control strip 236 is configured to control a temperature ofthe biological samples within the corresponding sample channels206A-206D along the thermal-control area 234. The temperature may becontrolled during an amplification protocol in which the biologicalsamples experience an increase/decrease in temperature in accordancewith a predetermined schedule in order to amplify the biological sample.In such embodiments, the biological samples may be loaded into thesample ports 204A-204D with an amplification (e.g., PCR) mix ofreagents. Alternatively, the amplification mix may be deliveredseparately to the sample-preparation regions 232 through the fluidicnetwork 202. For example, the sample-preparation regions 232 may be inflow communication with another channel (not shown) through which theamplification mix may be delivered.

In some embodiments, the flow-control system 200 includes a storageassembly or module 238. As shown, the storage assembly 238 includes aplurality of reservoirs 240-244. Each of the reservoirs 240-244 isconfigured to hold a reaction component that may be used during apredetermined assay protocol (e.g., SBS protocol). Each of thereservoirs 240-244 may be in flow communication with a correspondingport through one of the reservoir channels 220. As described herein, therotary valve 216 is configured to rotate to different valve positions inaccordance with a predetermined schedule to fluidically connect the feedchannel 224 to other channels of the fluidic network 202.

In some embodiments, the flow-control system 200 may also includechannel valves 246, 248. As shown, each of the sample channels 206A-206Dis coupled to a pair of the channel valves 246, 248. The correspondingsample-preparation region 232 for each sample channel 206A-206D extendsbetween the corresponding pair of channel valves 246, 248. Each pair ofchannel valves 246, 248 is configured to seal the correspondingbiological sample within the sample-preparation region 232 as thebiological sample experiences different conditions. For example, thechannel valves 246, 248 may seal the corresponding biological sampletherebetween as the biological sample experiences thermocycling of a PCRprotocol.

To induce flow throughout the fluidic network 202, the flow-controlsystem 200 may include a pump assembly 332. In the illustratedembodiment, the flow-control system 200 includes only a single pump 333that is located downstream from the reaction chamber 326 and draws orsucks the fluid through the fluidic network 202. In alternativeembodiments, one or more pumps may be used to push the fluid through thefluidic network 202. For example, one or more pumps may be fluidicallypositioned upstream with respect to the reservoirs 240-243 and/or thereservoir 244. The sample ports 204A-204D may also be fluidicallyconnected to an upstream pump that induces flow of the biological sampletoward the sample channel 208.

FIGS. 3-8 illustrate different valving mechanisms through which theflow-control system 200 (FIG. 2 ) may control (e.g., regulate) flowthrough the fluidic network 202 (FIG. 2 ). More specifically, FIGS. 3and 4 illustrate a cross-section of a valving mechanism 250 thatincludes the channel valve 246. Although the following is with respectto the channel valve 246, the channel valve 248 (FIG. 2 ) and othervalves may include similar or identical features. As shown, themicrofluidic body 212 includes a plurality of layers 252-254 that arestacked side-by-side. The layers 252-254 may be printed circuit board(PCB) layers. One or more of the layers 252-254 may be etched such that,when the layers 252-254 are stacked side-by-side, the microfluidic body212 forms the sample channel 206. The sample channel 206 includes avalve or interior cavity 256.

The channel valve 246 is configured to regulate flow of a fluid throughthe sample channel 206. For example, the channel valve 246 may permitmaximum clearance so that the fluid may flow unimpeded. The channelvalve 246 may also impede the flow of fluid therethrough. As usedherein, the term “impede” may include slowing the flow of fluid orentirely blocking the flow of fluid. As shown, the sample channel 206includes first and second ports 258, 260 that are in flow communicationwith the valve cavity 256. the channel is configured for fluid to flowinto the valve cavity 256 through the first port 258 and out of thevalve cavity 256 through the second port 260. In the illustratedembodiment, the channel valve 246 constitutes a flexible membrane thatis capable of being flexed between first and second conditions. Theflexible membrane is in the first condition in FIG. 3 and in the secondcondition in FIG. 4 . In particular embodiments, the flexible membraneis a flexible layer. The flexible layer is configured to be pushed intothe valve cavity 256 and cover the first port 258 to block the flow offluid therethrough. In alternative embodiments, the channel valve 246may be another physical element that is capable of moving betweendifferent conditions or positions to regulate flow of the fluid.

The flow-control system 200 (FIG. 2 ) may also include a valve actuator262 that is configured to activate the channel valve 246. For instance,the valve actuator 262 may flex the flexible membrane between the firstand second conditions. The valve actuator 262 includes an elongated body264, such as a post or rod, that extends through an access hole oropening 266. The access hole 266 permits the valve actuator 262 todirectly engage the channel valve 246, which is a flexible membrane inthe illustrated embodiment. In FIG. 5 , the valve actuator 262 is in afirst state or position. In FIG. 6 , the valve actuator 262 is in asecond state or position. In the second position, the valve actuator 262is engaged with the channel valve 246 and has been moved a distancetoward the first port 258. The valve actuator 262 may deform the channelvalve 246 such that the channel valve 246 covers the first port 258. Assuch, fluid flow through the first port 258 is blocked by the channelvalve 246.

FIGS. 5 and 6 illustrate a cross-section of a valving mechanism 270 thatincludes a channel valve 272. In some embodiments, the channel valve 246(FIG. 2 ) may be substituted with the channel valve 272. The valvingmechanism 270 may be similar to the valving mechanism 250. For example,the valving mechanism includes the channel valve 272 and a valveactuator 274. The valve actuator 274 has an elongated body 276, such asa nozzle, that extends into an access hole or opening 278. The accesshole 278 may constitute a closed or sealed chamber. In an exemplaryembodiment, the channel valve 272, which may be a flexible membrane, ispneumatically activated by the valve actuator 274. More specifically,the valve actuator 274 is configured to provide a fluid (e.g., air) toincrease a pressure within the closed chamber thereby causing thechannel valve 272 to deform. When the channel valve 272 is deformed, thechannel valve may cover a port 277 of a sample channel 279 therebyblocking flow through the sample channel 279.

FIGS. 7 and 8 illustrate a valving mechanism 280 that includes a channelvalve 282. The valving mechanism 280 may include similar features as thevalving mechanisms 250 (FIG. 3 ), 270 (FIG. 5 ). The channel valve 282is rotatably engaged to a valve actuator 284. The channel valve 282 is aplanar body that is shaped to permit flow through a sample channel 286when in a first rotational position (shown in FIG. 7 ) and block flowthrough the sample channel 286 when in a second rotational position(shown in FIG. 8 ). More specifically, the channel valve 282 may cover aport 288 when in the second rotational position.

FIG. 9 illustrates a cross-section of the rotary valve 216 that isoperably engaged with a valve actuator 290. The rotary valve 216 isslidably engaged to the body side 214 of the microfluidic body 212. Thevalve actuator 290 is configured to rotate the rotary valve 216 aboutthe axis 299 to designated valve positions (or rotational positions) tofluidically couple different channels of the fluidic network 202 (FIG. 1). The rotary valve 216 includes a valve body 292 having a fluidic side294 and an operative side 296. The operative side 296 may include amechanical interface 298 that is configured to engage the valve actuator290. In the illustrated embodiment, the mechanical interface 298includes a planar body or fin that coincides with the axis 299. Thevalve actuator 290 includes a slot 300 that is configured to receive themechanical interface 298 such that the valve actuator 290 operablyengages the rotary valve 216. More specifically, the valve actuator 290may engage the rotary valve 216 so that the valve actuator 290 iscapable of rotating the rotary valve 216 about the axis 299.

The body side 214 includes the supply port 210 and the feed port 226.The body side 214 also includes the reservoir ports 222A-222E (shown inFIG. 10 ). The flow channel 218 extends between first and second channelports 306, 308. The first and second channel ports 306, 308 open to thefluidic side 294 of the valve body 292. In an exemplary embodiment, therotary valve 216 includes only two channel ports 306, 308 and only oneflow channel 218. However, in other embodiments, the rotary valve 216may include more than two channel ports and/or more than one flowchannel. Such embodiments may enable fluidically connecting more thantwo channels at a single rotational position of the rotary valve 216.

As shown in FIG. 9 , the feed port 226 is aligned and fluidicallycoupled to the channel port 308, and the supply port 210 is aligned andfluidically coupled to the channel port 306. Based on the rotationalposition of the rotary valve 216, the channel port 306 may also befluidically coupled to one of the reservoir ports 222A-222E. As notedabove, the rotary valve 216 is configured to rotate about the axis 299.In some embodiments, the feed port 226 and the channel port 308 arepositioned such that the feed port 226 and the channel port 308 arealigned with the axis 299. More specifically, the axis 299 extendsthrough each of the feed port 226 and the channel port 308.

When the valve actuator 290 is operably engaged to the rotary valve 216,the valve actuator 290 may apply an actuator force 310 in a directionagainst the body side 214. In such embodiments, the actuator force 310may be sufficient to seal the flow channel 218 between the channel ports306, 308 and to seal the reservoir ports 222 and/or the supply port 210.

Accordingly, the rotary valve 216 may fluidically couple the feed port226 and the supply port 210 at a first rotational position andfluidically couple the feed port 226 and a corresponding reservoir port222 at a second rotational position. When the rotary valve 216 isrotated between the different rotational positions, the rotary valve 216effectively changes a flow path of the fluidic network.

The fluid may flow in either direction through the flow channel 218. Forexample, a system pump (not shown), such as the system pump 119 (FIG. 1) may be in flow communication with the feed port 226. The system pumpmay generate a suction force that pulls the fluid through the supplyport 210 (or a corresponding reservoir port 222) into the flow channel218 and through the feed port 226. Alternatively, the system pump mayprovide a positive pressure that displaces fluid within the flow channel218 such that the fluid flows through the feed port 226 into the flowchannel 218 and through the supply port 210 (or a correspondingreservoir port 222).

FIG. 10 is a top-down view of the body side 214 illustrating the supplyport 210, the feed port 226, and reservoir ports 222A-222E. In FIG. 10 ,the flow channel 218 is represented in two different rotationalpositions, but it is understood that the flow channel 218 may have otherrotational positions. The rotational positions of the flow channel 218correlate to valve positions of the rotary valve 216 (FIG. 2 ). Thereservoir ports 222A-222E are fluidically coupled to correspondingreservoirs through the corresponding reservoir channel. For example, thereservoir port 222A is fluidically coupled to the reservoir 243; thereservoir port 222B is fluidically coupled to the reservoir 242; thereservoir port 222C is fluidically coupled to the reservoir 241; thereservoir port 222D is fluidically coupled to the reservoir 240; and thereservoir port 222E is fluidically coupled to the reservoir 244. Asdescribed above, based on a rotational position of the rotary valve 216(FIG. 2 ), the flow channel 218 may fluidically couple the feed port 226to the supply port 210 or to one of the corresponding reservoir ports222A-222E.

Table 1 illustrates various stages of a sequencing-by-synthesis (SBS)protocol. In an exemplary embodiment, the reservoir 244 includes ahydrogenation buffer, the reservoir 243 includes a nucleotides solution,the reservoir 242 includes a wash solution, and the reservoir 241includes a cleaving solution. Although Table 1 provides a schedule foran SBS protocol, it should be understood that various schedules may beprovided based on the desired assay protocol. In the following example,the biological samples have been amplified within the correspondingsample-preparation region 232 (FIG. 2 ) in accordance with a PCRprotocol.

At stage 1, the flow channel 218 has a valve position that fluidicallycouples the supply port 210 and the feed port 226. At stage 1, thechannel valves 246, 248 (FIG. 2 ) that are coupled to the sample channel206A are deactivated (e.g., in the first condition) to permit a firstbiological sample to flow through the sample channel 206A and the samplechannel 208. The channel valves 246, 248 that are coupled to the samplechannels 206B-206D, however, are activated to seal the second, third,and fourth biological samples within the correspondingsample-preparation region 232. Accordingly, at stage 1, the pumpassembly 332 (FIG. 2 ) may induce flow of the first biological sampleinto the flow channel 218. At stage 2, the rotary valve 216 is rotatedto a second valve position, while the first biological sample is storedwithin the flow channel 218, so that the flow channel 218 fluidicallycouples the reservoir port 222E and the feed port 226. In the secondvalve position, the pump assembly 332 may induce a flow of the fluidwithin the flow channel 218 such that the first biological sample flowsthrough the reservoir port 222E and into the hydrogenation buffer.

At stage 3, the rotary valve 216 is rotated back to the first valveposition and the channel valves 246, 248 are selectively activated sothat the second biological sample is permitted to flow into the flowchannel 218 while the third and fourth biological samples are sealedwithin the sample-preparation regions 232. At stage 4, the rotary valve216 is rotated back to the second valve position, while the secondbiological sample is stored within the flow channel 218, and the secondbiological sample is added to the hydrogenation buffer with the firstbiological sample. During stages 5-8, the third and fourth biologicalsamples are removed from the corresponding sample-preparation regionsand added to the hydrogenation buffer. Accordingly, four biologicalsamples may be stored within a single reservoir having hydrogenationbuffer. While within the reservoir 243, reactions may occur with thebiological samples and the hydrogenation buffer that prepare thebiological samples for SBS sequencing.

At stage 9, the pump assembly 332 draws the combined biologicalsamples/hydrogenation buffer through the reservoir port 222E, throughthe flow channel 218, through the feed port 226, and into the reactionchamber 326 (FIG. 2 ). The biological samples may be immobilized tosurfaces that define the reaction chamber. For example, clusters may beformed that include the biological samples. Stages 10-13 represent asequencing cycle. At stage 10, the rotary valve 216 may be at a thirdvalve position so that a nucleotides solution may be drawn through theflow channel 218 and into the reaction chamber. At such time, anucleotide may be incorporated into the corresponding biological samples(e.g., primers annealed to template nucleic acids). At stage 11, therotary valve 216 may be at a fourth valve position so that a washsolution may flow through the reaction chamber and carry the nucleotidessolution away from the reaction chamber. After stage 11, the reactionchamber may be imaged by the imaging detector, such as the detectiondevice 404 (FIG. 11 ). The color of light emitted from the clusters maybe used to identify the bases incorporated by the clusters. At stage 12,the rotary valve 216 may be at a fourth valve position so that acleaving solution may flow through the reaction chamber and thefluorophores (and, if present, reversible terminator moieties) may beremoved from the clusters. At stage 13, the rotary valve 216 may be atthe third valve position again and the wash solution may flow throughthe reaction chamber to remove the cleaving solution. Stages 10-13 maybe repeated until completion of the sequencing and/or until reagents aredepleted.

TABLE 1 Type of Fluid Flowing Port into Flow Channel Flow DirectionStage 210 1st Biological Sample Toward feed 1 port 226 Stage 222E 1stBiological Sample Away from feed 2 port 226 Stage 210 2nd BiologicalSample Toward feed 3 port 226 Stage 222E 2nd Biological Sample Away fromfeed 4 port 226 Stage 210 3rd Biological Sample Toward feed 5 port 226Stage 222E 3rd Biological Sample Away from feed 6 port 226 Stage 210 4thBiological Sample Toward feed 7 port 226 Stage 222E 4th BiologicalSample Away from feed 8 port 226 Stage 222E Combined Biological Towardfeed 9 Samples + port 226 Hydrogenation Buffer Stage 222A NucleotidesSolution Toward feed 10 port 226 Stage 222B Wash Solution Toward feed 11port 226 Stage 222C Cleaving Solution Toward feed 12 port 226 Stage 222BWash Solution Toward feed 13 port 226 Repeat Stages 10-13 untildetection complete

FIG. 11 illustrates a cross-section of a portion of a detection assembly400. In the illustrated embodiment, the detection assembly 400 isintegrally formed with the flow cell 320. More specifically, thedetection assembly includes a detection device 404, which is positionedadjacent to the flow cell 320 and the reaction chamber 326. The flowcell 320 may be mounted to the detection device 404. In the illustratedembodiment, the flow cell 320 is affixed directly to the detectiondevice 404 through one or more securing mechanisms (e.g., adhesive,bond, fasteners, and the like). In some embodiments, the flow cell 320may be removably coupled to the detection device 404. In particularembodiments, the detection device 404 is configured to detect lightsignals from the reaction chamber 326. Accordingly, the detection device404 may be referred to as an imaging detector in some embodiments.

In the illustrated embodiment, the detection device 404 includes adevice base 425. In particular embodiments, the device base 425 includesa plurality of stacked layers (e.g., silicon layer, dielectric layer,metal-dielectric layers, etc.). The device base 425 may include a sensorarray 424 of light sensors 440, a guide array 426 of light guides 462,and a reaction array 428 of reaction recesses 408 that havecorresponding reaction sites 414. In certain embodiments, the componentsare arranged such that each light sensor 440 aligns with a single lightguide 462 and a single reaction site 414. However, in other embodiments,a single light sensor 440 may receive photons through more than onelight guide 462 and/or from more than one reaction site 414. As usedherein, a single light sensor may include one pixel or more than onepixel. The detection device 404 may be manufactured usingcomplementary-metal-oxide semiconductor (CMOS) technology. In particularembodiments, the detection device 404 is a CMOS imaging detector.

It is noted that the term “array” or “sub-array” does not necessarilyinclude each and every item of a certain type that the detection devicemay have. For example, the sensor array 424 may not include each andevery light sensor in the detection device 404. Instead, the detectiondevice 404 may include other light sensors (e.g., other array(s) oflight sensors). As another example, the guide array 426 may not includeeach and every light guide of the detection device. Instead, there maybe other light guides that are configured differently than the lightguides 462 or that have different relationships with other elements ofthe detection device 404. As such, unless explicitly recited otherwise,the term “array” may or may not include all such items of the detectiondevice.

In the illustrated embodiment, the flow cell 320 includes a sidewall 406and a flow cover 410 that is supported by the sidewall 406 and othersidewalls (not shown). The sidewalls are coupled to the detector surface412 and extend between the flow cover 410 and the detector surface 412.In some embodiments, the sidewalls are formed from a curable adhesivelayer that bonds the flow cover 410 to the detection device 404.

The flow cell 320 is sized and shaped so that the reaction chamber 326exists between the flow cover 410 and the detection device 404. Asshown, the reaction chamber 326 may include a height H₁. By way ofexample only, the height H₁ may be between about 50-400 μm (microns) or,more particularly, about 80-200 μm. In the illustrated embodiment, theheight H₁ is about 100 μm. The flow cover 410 may include a materialthat is transparent to excitation light 401 propagating from an exteriorof the detection assembly 400 into the reaction chamber 326. As shown inFIG. 7 , the excitation light 401 approaches the flow cover 410 at anon-orthogonal angle. However, this is only for illustrative purposes asthe excitation light 401 may approach the flow cover 410 from differentangles. The reaction chamber 326 is sized and shaped to direct a fluidalong the detector surface 412. The height H₁ and other dimensions ofthe reaction chamber 326 may be configured to maintain a substantiallyeven flow of a fluid along the detector surface 412. The dimensions ofthe reaction chamber 326 may also be configured to control bubbleformation.

The sidewalls 406 and the flow cover 410 may be separate components thatare coupled to each other. In other embodiments, the sidewalls 406 andthe flow cover 410 may be integrally formed such that the sidewalls 406and the flow cover 410 are formed from a continuous piece of material.By way of example, the flow cover 410 (or the flow cell 320) maycomprise a transparent material, such as glass or plastic. The flowcover 410 may constitute a substantially rectangular block having aplanar exterior surface and a planar inner surface that defines thereaction chamber 326. The block may be mounted onto the sidewalls 406.Alternatively, the flow cell 320 may be etched to define the flow cover410 and the sidewalls 406. For example, a recess may be etched into thetransparent material. When the etched material is mounted to thedetection device 404, the recess may become the reaction chamber 326.

The detection device 404 has a detector surface 412 that may befunctionalized (e.g., chemically or physically modified in a suitablemanner for conducting designated reactions). For example, the detectorsurface 412 may be functionalized and may include a plurality ofreaction sites 414 having one or more biomolecules immobilized thereto.The detector surface 412 has an array of reaction recesses or open-sidedreaction recesses 408. Each of the reaction recesses 408 may include oneor more of the reaction sites 414. The reaction recesses 408 may bedefined by, for example, an indent or change in depth along the detectorsurface 412. In other embodiments, the detector surface 412 may besubstantially planar.

As shown in FIG. 11 , the reaction sites 414 may be distributed in apattern along the detector surface 412. For instance, the reactionssites 414 may be located in rows and columns along the detector surface412 in a manner that is similar to a microarray. However, it isunderstood that various patterns of reaction sites may be used. Thereaction sites may include biological or chemical substances that emitlight signals. For example, the biological or chemical substances of thereactions sites may generate light emissions in response to theexcitation light 401. In particular embodiments, the reaction sites 414include clusters or colonies of biomolecules (e.g., nucleic acids) thatare immobilized on the detector surface 412.

FIG. 12 is a flowchart of a method 470. In some embodiments, the method470 may include preparing a biological sample and/or detectingdesignated reactions of the biological sample for analysis. The method470 may, for example, employ structures or aspects of variousembodiments (e.g., systems and/or methods) discussed herein. In variousembodiments, certain steps may be omitted or added, certain steps may becombined, certain steps may be performed simultaneously, certain stepsmay be performed concurrently, certain steps may be split into multiplesteps, certain steps may be performed in a different order, or certainsteps or series of steps may be re-performed in an iterative fashion.

The method 470 may be performed or executed using a flow-control systemthat is similar or identical to the flow-control system 200 (FIG. 2 ).The method 470 includes rotating (at 472) a rotary valve to a firstvalve position. The rotary valve has at least one flow channel. In thefirst valve position, the flow channel may be in flow communication witha sample channel (or other reservoir of the flow-control system) and inflow communication with a reaction chamber such that the flow channelfluidically couples the sample channel and the reaction chamber. Forexample, the rotary valve may have first and second channel ports. Thefirst channel port may be aligned with a port (e.g., a supply port orreservoir port) and the second channel port may be aligned with a feedport. When the rotary valve is in the first valve position, other portsmay be sealed by the rotary valve such that fluid is blocked fromflowing through the other ports.

The method 470 may also include flowing (at 474) a biological samplefrom a sample channel (or a first reservoir) into the flow channel whenthe rotary valve is in the first valve position. For example, thebiological sample may flow through a supply port into the flow channelof the rotary valve. As another example, the biological sample may bedisposed within a reservoir, such as a reservoir that containshydrogenation buffer. The biological sample (with hydrogenation buffer)may flow through a reservoir port and into the flow channel.

Optionally, the biological sample may continue to flow (at 476) into thereaction chamber. Alternatively, the method 470 may include rotating (at478) the rotary valve to a second valve position while the biologicalsample is disposed within the flow channel. In the second valveposition, the flow channel may be fluidically coupled to anotherreservoir, such as a reservoir that contains a hydrogenation buffer. At480, the biological sample within the flow channel may be induced toflow (e.g., by a pump assembly) into the reservoir. The method 470 maythen include repeating steps 472, 474, 478, and 480 until each of thedesired biological samples is disposed within a common reservoir. At482, the biological samples with the hydrogenation buffer maysimultaneously flow through the flow channel and into the reactionchamber.

Accordingly, one or more biological samples may be directed into thereaction chamber utilizing the rotary valve. In alternative embodiments,the biological sample (or samples) has a direct channel to the reactionchamber and does not flow through the rotary valve. Optionally, themethod 470 may begin cycling through designated operations to conductthe designated reactions, such as the operations described with respectto Table 1. For example, the rotary valve may be rotated (at 484) toanother valve position to fluidically couple the reaction chamber to adesignated reservoir. At 486, a reaction component may flow into thereaction chamber to interact with the biological sample(s) therein.Optionally, at 488, the method 470 includes detecting the designatedreactions within the reaction chamber. The method 470 may then return tostep 484.

FIG. 13 is a plan view of a rotary valve 500 formed in accordance withan embodiment that is rotatably mounted to a body side 502 of amicrofluidic body 504. The rotary valve 500 may include similar featuresas the rotary valve 216 (FIG. 2 ). The microfluidic body 504 includes aplurality of reservoirs 506-510 that are configured to hold reactioncomponents and/or biological samples. More specifically, the reservoirs506-509 hold first, second, third, and fourth biological samples (orsample liquids). The reservoir 510 includes a hydrogenation buffer. Eachof the reservoirs 506-510 is fluidically coupled to a corresponding portthrough a respective reservoir channel 516-520, which are represented bylines in FIG. 13 . As shown, the ports include reservoir or supply ports526-530 that open to the body side 502 and are in flow communicationwith the reservoirs 506-510. The microfluidic body 504 also includes afeed port 524 (shown in FIG. 13 ) that opens to the body side 502.

The rotary valve 500 includes a valve body 512 having a fluidic side 513(shown in FIG. 14 ) that engages the body side 502 and an oppositeoperative side 514. The valve body 512 includes first, second, third,and fourth flow channels 536-539. Each of the flow channels 536-539 isconfigured to hold a biological sample during an amplification or PCRprotocol. Each of the flow channels 536-539 has a common channel port(or outlet port) 544 that is centrally located. In other embodiments,the flow channels 536-539 do not share the same channel port. The commonchannel port 544 is located at an axis 542 about which the rotary valve500 rotates. The flow channels 536-539 include respective first channelports (or inlet ports) 546-549. Accordingly, each of the flow channels536-539 extends from a respective first channel port 546-549 to a commonchannel port 544. Similar to the rotary valve 216 (FIG. 2 ), the rotaryvalve 500 is configured to rotate to different valve positions tofluidically couple reservoirs and channels. Unlike the rotary valve 500,however, the rotary valve 500 may be used during an amplificationprotocol. More specifically, the valve body 512 may engage athermocycler 570 (shown in FIG. 14 ) while the biological samples areheld within the flow channels 536-539.

In some embodiments, the flow channels 536-539 may have anti-diffusionsegments 545. The anti-diffusion segments 545 are configured to reducethe likelihood of diffusion occurring as the biological sample withinthe flow channels 536-539 is subjected to a PCR protocol. For example,the flow channels 536-539 shown in FIG. 13 have non-linear paths anddimensions that change along the path. More specifically, the flowchannels 536-539 having serpentine or wavy paths that wrap back andforth as the flow channel extends from the corresponding first channelport toward the common channel port 544. The first channel ports 546-549have radially outward locations. In addition to the shape of the flowchannels 536-539, the flow channels 536-539 have dimensions that reduceas the flow channel 536-539 extends from the corresponding first channelport to the common channel port 544. In other embodiments, theanti-diffusion segments 545 do not have a serpentine path. Segments ofthe flow channels 536-539 that do not include the anti-diffusion segment545 may be referred to as the sample-preparation region 543 thatrepresents a portion of the corresponding flow channel where thebiological sample may experience different conditions, such astemperature changes. It should be understood, however, that thebiological sample may also exist within the anti-diffusion segments 545for at least some embodiments.

FIG. 14 illustrates a side cross-section of the rotary valve 500 whenthe thermocycler 570 is mounted to the operative side 514. In someembodiments, the thermocycler 570 may provide a mounting force 572 thatpresses the valve body 512 against the body side 502 of the microfluidicbody 504. Although not shown in FIG. 14 , the valve body 512 may includeone or more mechanical interfaces (e.g., non-planar features, such asfins) that are engaged by the thermocycler 570. The thermocycler 570 isconfigured to control a temperature of the flow channels 536-539. Inparticular embodiments, the thermocycler 570 simultaneously controls thetemperature of each of the flow channels 536-539. In other embodiments,the thermocycler 570 may selectively engage less than all of the flowchannels at a single time.

As shown in FIG. 14 , the common channel port 544 is fluidically coupledto the feed port 524. The axis 542 extends through the common channelport 544 and the feed port 524. The first channel port 547 of the flowchannel 537 is fluidically coupled to a reservoir port 527. However, thefirst channel port 549 of the flow channel 539 is sealed by the bodyside 502. Accordingly, in the valve position shown in FIG. 14 , fluid(e.g., fluid containing the biological sample) may flow from thereservoir 507 (FIG. 13 ) and into the flow channel 537.

FIGS. 15A-15L are plan views of the rotary valve 500 and illustratedifferent valve positions where different operations may occur. Toprepare for the amplification protocol, a system controller, such as thesystem controller 180 (FIG. 1 ), is configured to selectively control apump assembly (not shown) and the rotary valve 500. The pump assemblymay be similar to the pump assembly 332 and include one or more flowpumps. In some embodiments, a single pump may be downstream with respectto the rotary valve 500 and be configured to pull fluids through thecommon channel port 544 (FIG. 15A).

Optionally, the flow channels 536-539 (FIG. 15A) may be primed with afluid prior to receiving the biological sample. For example, FIGS.15A-15D show the first channel port of a corresponding flow channelfluidically coupled to the reservoir port 530, which is in flowcommunication with the reservoir 510. Accordingly, the first channelport of each flow channel may be individually coupled to the reservoir510. When the flow channel is in flow communication with the reservoir510, the system controller may selectively activate the pump assembly toinduce flow of the reaction component within the reservoir 510 so thatthe reaction component flows into the corresponding flow channel.

Accordingly, after FIG. 15D, each of the flow channels 536-539 is primedwith a reaction component. Although the reaction component is associatedwith the reservoir 510, other reaction components may be used to primethe flow channels 536-539. For example, the flow channels 536-539 mayfluidically couple to a separate reservoir (not shown) that contains,for example, water or a buffer solution. In the illustrated embodiment,each of the flow channels 536-539 separately couples to the reservoir510. In alternative embodiments, one or more of the flow channels536-539 may simultaneously couple to the reservoir 510 or to separatereservoirs.

After the flow channels 536-539 have been primed, the biological samplefrom the reservoirs 506-509 (FIG. 15E) may be loaded into the flowchannels 536-539 (FIG. 15E), respectively. For example, as shown in FIG.15E, the flow channel 538 is fluidically coupled to the reservoir port528 and, as such, in flow communication with the reservoir 508. At thistime, the flow channels 536, 537, and 539 are covered by the body side502. The pump assembly may induce a flow of the biological sample withinthe reservoir 508 so that the biological sample flows into the flowchannel 538. The amount of flow may be based on the amount of fluidwithin the reservoir 508. After the biological sample has been loadedinto the flow channel 538, the rotary valve 500 may be selectivelyrotated and the pump assembly, in a similar manner, may be selectivelyactivated to load the biological samples that are the reservoirs 506,507, and 509 into the flow channels 536, 537, and 539, respectively, asshown in FIGS. 15F-15H.

With the biological samples loaded within the respective flow channels536-539, the rotary valve 500 may be selectively rotated such that eachof the first channel ports 546-549 is covered (or sealed) by the bodyside 502 of the microfluidic body 504. The valve position in which thefirst channel ports 546-549 are sealed is shown in FIG. 151 . Thethermocycler 570 (FIG. 14 ) may then be controlled to cycle throughtemperature changes in accordance with a designated amplificationprotocol. Although the flow channels 536-539 are only sealed at one end,the pump assembly and the anti-diffusion segments 545 may resistmovement and/or diffusion of the biological sample (e.g., PCR plug) intoor through the feed port 524 (FIG. 14 ).

After the amplification protocol, the biological samples may be loadedinto a common reservoir. For instance, as shown in FIGS. 15J-15L, thebiological samples within the flow channels 536-538 may be fluidicallycoupled to the reservoir 510. The pump assembly may be selectivelyoperated to induce flow of the biological sample into the reservoir 510.Although not shown, the flow channel 536 may also be fluidically coupledto the reservoir 510 so that the biological sample within the flowchannel 536 may be loaded into the reservoir 510. Accordingly, each ofthe biological samples from the reservoir 506-509 may be loaded into acommon reservoir 510 after the amplification protocol. The pump assemblymay then be selectively activated to induce flow of the mixed biologicalsamples through the feed port 524. The biological samples may befluidically delivered to a reaction chamber, such as the reactionchamber 326 (FIG. 2 ). The biological samples may then undergodesignated reactions as described herein. In particular embodiments, thebiological samples may be used during an SBS protocol.

FIG. 16 is a plan view of a rotary valve 600 formed in accordance withan embodiment that is mounted to a body side 616 of a microfluidic body618. The rotary valve 600 may include similar features as the rotaryvalve 216 (FIG. 2 ) and the rotary valve 500 (FIG. 13 ). The rotaryvalve 600 includes a valve body 602 having flow channels 604-606. Eachof the flow channels 604-606 extends between a first channel port (orinlet port) 608 and a second channel port (or outlet port) 610. Unlikethe rotary valve 500, the flow channels 604-606 are not in flowcommunication with a common channel port.

In the illustrated embodiment, each of the flow channels 604-606 is inflow communication with an upstream channel 612 and a downstream channel614. In FIG. 16 , the rotary valve 600 is in a valve position such thateach of the flow channels 604-606 may receive a biological sample fromthe corresponding upstream channel 612. For instance, the flow channels604-606 may simultaneously receive the corresponding biological sample.The flow of the biological samples into the flow channels 604-606 may beinduced by a common pump. For example, the downstream channels 614 maymerge together and fluidically coupled to a single pump. Alternatively,separate pumps may be fluidically coupled to the flow channels 604-606.

FIG. 17 is a plan view of the rotary valve 600 after the rotary valvehas been rotated to a valve position in which the first and secondchannel ports 608, 610 for each of the flow channels 604-606 is sealedby the body side 616 of the microfluidic body 618. In the valve positionshown in FIG. 17 , a thermocycler (not shown) may engage the valve body602 to control a temperature experienced within the flow channels604-606. As such, the biological samples may undergo an amplificationprotocol as described herein. Unlike the embodiment shown in FIGS. 13-15, the flow channels 604-606 are sealed at both ends to reduce thelikelihood of diffusion and movement of the PCR plug.

FIG. 18 is a plan view of a rotary valve 620 formed in accordance withan embodiment. The rotary valve 620 may be similar or identical to therotary valve 600 (FIG. 16 ) and include a plurality of flow channels624-626. As shown, the rotary valve 600 is separated into threethermal-control areas or zones 634-636. The thermal-control areas634-636 are represented by pie-shaped areas that are indicated by dashedlines. Each thermal-control area 634-636 represents a differenttemperature range controlled by one or more thermocyclers (not shown).More specifically, after the biological samples are loaded into the flowchannels 624-626, the rotary valve 620 may be selectively rotated todifferent positions. The flow channel within the thermal-control area634 may experience a designated temperature for denaturing nucleicacids. The flow channel within the thermal-control area 635 mayexperience a designated temperature for an annealing-extension stage,and the flow channel within the thermal-control area 636 may experiencea designated temperature for a pre-heating and/or temperature holdingstage. The system controller may selectively rotate the rotary valve 620to three different valve positions to cycle the biological samplesthrough multiple PCR amplification stages. Thus, unlike the flowchannels of the rotary valve 600, the flow channels 624-626 experiencedifferent temperatures.

FIG. 19 is a flowchart illustrating a method 650. In some embodiments,the method 650 may include preparing a biological sample and,optionally, detecting designated reactions of the biological sample foranalysis. The method 650 may, for example, employ structures or aspectsof various embodiments (e.g., systems and/or methods) described herein,such as the embodiments described with respect to FIGS. 13-18 . Invarious embodiments, certain steps may be omitted or added, certainsteps may be combined, certain steps may be performed simultaneously,certain steps may be performed concurrently, certain steps may be splitinto multiple steps, certain steps may be performed in a differentorder, or certain steps or series of steps may be re-performed in aniterative fashion.

The method 650 may include providing (at 652) a microfluidic body and arotary valve. The microfluidic body may have a body side and a fluidicnetwork that includes a supply port, such as the reservoir ports526-529, and a feed port. The supply port may open to the body side. Therotary valve may be rotatably mounted to the body side and have a firstchannel port, a second channel port, and a flow channel that extendsbetween the first channel port and the second channel port. In someembodiments, multiple flow channels may be used in which the flowchannels have separate second channel ports, such as the embodiments ofFIGS. 16-18 , or share the second channel port, such as the embodimentof FIGS. 13-15 . In such embodiments in which the second channel port isshared, the second channel port may be referred to as a common channelport.

The method 650 may include rotating (at 654) the rotary valve to a firstvalve position at which the first channel port is in flow communicationwith the supply port of the microfluidic body. The method 650 may alsoinclude flowing (at 656) a biological sample through the first channelport and into the flow channel when the rotary valve is in the firstvalve position. The biological sample may flow in a direction that isfrom the first channel port and toward the second channel port. Theflowing (at 656) may include selectively controlling the flow rateand/or duration of the flowing such that the biological sample does notsubstantially flow past the second channel port or the feed port. Forembodiments that include multiple flow channels, such as the rotaryvalve 500, the steps 654 and 656 may be repeated until each of the flowchannels has a corresponding biological sample therein. However, therotating (at 654) for each flow channel is not to the same valveposition. More specifically, when the biological sample is flowed into acorresponding flow channel, the other flow channels may be sealed at oneend or both ends.

The method 650 may also include rotating (at 658) the rotary valve to asecond valve position with the biological sample within the flow channelsuch that the first channel port is sealed by the body side andperforming (at 660) a thermocycling operation to change a temperature ofthe biological sample in the flow channel to a select temperature. Theperforming (at 660) may be in accordance with a predetermined schedule.For example, the schedule may be to execute a PCR operation in order toamplify the biological sample for subsequent analysis.

Optionally, after the performing (at 660), the biological sample orbiological samples may be loaded (at 662) into a reservoir. For example,the reservoir may include hydrogenation buffer solution that preparesthe biological sample for subsequent analysis. At 664, the biologicalsample (or the combined biological samples) may be delivered to areaction chamber for subsequent analysis at 666.

FIG. 20 is a perspective view of flow-control system 700 formed inaccordance with an embodiment that includes a microfluidic body 702 anda rotary valve 704. Unlike the rotary valves 500 (FIG. 13 ), 600 (FIG.16 ), and 620 (FIG. 18 ), amplification does not occur solely within therotary valve 704. Instead, amplification occurs at least partiallywithin the microfluidic body 702. More specifically, the microfluidicbody 702 has a first body side 706 (shown in FIG. 22 ) and a second bodyside 708 (shown in FIG. 22 ) that face in opposite directions. Themicrofluidic body 702 has a fluidic network 705 that includes aplurality of sample reservoirs 711-714, a plurality of supply channels721-724 with corresponding inlet ports 731-734, and a common outlet port736. The inlet ports 731-734 and the outlet port 736 open to the firstbody side 706 (FIG. 22 ).

The rotary valve 704 is rotatably mounted to the microfluidic body 702along first body side 706. In the illustrated embodiment, the rotaryvalve 704 has a first channel segment 726 and a second channel segment728. The first and second channel segments 726, 728 may open to afluidic side 709 (shown in FIG. 22 ) of the rotary valve 704.Alternatively, the first and second channel segments 726, 728 may extendbetween corresponding channel ports that open to the fluidic side 709.The first and second channel segments 726, 728 are separate from eachother and extend along only a portion of the fluidic side 709. In anexemplary embodiment, the second channel segment 728 is in flowcommunication with the outlet port 736 at any rotational position of therotary valve 704.

FIG. 20 shows the rotary valve 704 in a designated position in which thesample reservoir 711 is in flow communication with a pump assembly. Morespecifically, the first channel segment 726 is fluidically interposedbetween the inlet port 731 and the sample reservoir 711. The secondchannel segment 726 is fluidically interposed between the samplereservoir 711 and the outlet port 736. As such, the supply channel 721is in flow communication with a feed channel 756 through the firstchannel segment 726, the sample reservoir 711, and the second channelsegment 728.

Although not shown, the flow-control system 700 may include a pumpassembly that is configured to induce a flow of fluid through the inletport 731 and the first channel segment 726 into the sample reservoir711. The fluid may include a biological sample that is loaded within,for example, a remote reservoir (not shown) that is in flowcommunication with the supply channel 721. The flowing of the fluid andthe dimensions of the sample reservoir may be configured such that thebiological sample does not substantially exit the sample reservoir 711through the second channel segment 728. After the biological sample isloaded into the sample reservoir 711, the rotary valve 704 may beselectively rotated such that the first channel segment 726 and thesecond channel segment 728 fluidically couple to the sample reservoir712. The sample reservoir 712 may be loaded with a biological samplethat flows from the supply channel 722. In a similar manner, the samplereservoirs 713 and 714 may be loaded with a corresponding biologicalsample.

FIG. 21 is a perspective view of the flow-control system 700 after thesample reservoirs 711-714 have been loaded with corresponding biologicalsamples. In some embodiments, the rotary valve 704 includes gasreservoirs 741-744, which are shown in FIG. 20 . During an amplificationprotocol, the gas reservoirs 741-744 are configured to align with thesample reservoirs 711-714. For example, as shown in FIG. 22 , the samplereservoir 711 and the gas reservoir 741 combined to form asample-preparation chamber 751. Gas within the gas reservoir 741 mayfunction as a gas ballast in the sample-preparation chamber 751. Afterthermocycling, the biological samples may flow through the feed channel756 (FIG. 20 ) that is in flow communication with the outlet port 736.As described herein, the biological samples may be directed to areaction chamber, such as the reaction chamber 326 (FIG. 2 ), wheredesignated reactions may occur and be detected.

FIG. 23 is a schematic view of a system 800 formed in accordance with anembodiment. The system 800 may include similar features as the system100 (FIG. 1 ). For example, the system 800 includes a flow-controlsystem 802 having a fluidic network 804. The fluidic network 804 mayinclude a number of interconnected channels, ports, reservoirs, andother spatial regions that are configured to hold or have fluid flowtherethrough. For example, the fluidic network 804 includes rotaryvalves 806, 808. The rotary valve 806 is configured to be used during asample-preparation stage, and the rotary valve 808 is configured to beused during a sample-analysis stage. The rotary valves 806, 808 arefluidically coupled by an intermediate channel 810 of the fluidicnetwork 804. The fluidic network 804 also includes a feed channel 812, areaction chamber 814, and a waste reservoir 816. The flow-control system802 includes a pump assembly 818 that is in flow communication with thefluidic network 804. In the illustrated embodiment, the pump assembly818 includes a single pump, but may include multiple pumps in otherembodiments. The system 800 may include a microfluidic body (notindicated) having a body side 819. The rotary valves 806, 808 arerotatably mounted to the body side 819. The microfluidic body may alsoinclude or define the intermediate channel 810 and the feed channel 812.

The fluidic network 804 also includes a plurality of assay channels821-824 and a plurality of sample reservoirs 831-834. Each of the assaychannels 821-824 extends between corresponding first and second ports826, 828 and is configured to fluidically couple a corresponding samplereservoir to the intermediate channel 810. As shown, the assay channels821-824 extend through a thermal-control area 825. In the illustratedembodiment, the assay channels 821-824 have wavy paths through thethermal-control area 825. The portions of the assay channels 821-824that extend through the thermal-control area 825 may constitutesample-preparation regions 827. Alternatively or in addition to thenon-linear paths, the assay channels 821-824 may have differentdimensions to hold a designated volume of the corresponding biologicalsamples.

The rotary valve 806 is configured to move between multiple valvepositions. The rotary valve 806 includes a bridge channel 840 and a flowchannel 842. The bridge channel 840 and the flow channel 842 areconfigured to fluidically couple one of the sample reservoirs 831-834 tothe intermediate channel 810. For example, as shown in FIG. 23 , thebridge channel 840 fluidically couples a reservoir port (or supply port)853 of the sample reservoir 833 to the first port 826 of the assaychannel 823. Simultaneously, the flow channel 842 fluidically couplesthe second port 828 to an intermediate port 856. The intermediate port856 opens along the body side 819 and is in flow communication with theintermediate channel 810.

Accordingly, a system controller (not shown) may selectively rotate therotary valve 806 to fluidically couple the sample reservoirs 831-834 tothe corresponding assay channels 821-824, respectively. The systemcontroller may selectively control the pump assembly 818 to induce flowof the biological samples within the sample reservoirs such that thebiological samples are disposed within the sample-preparation regions827 of the assay channels 821-824.

When the biological sample (or samples) is located within thecorresponding assay channel, the rotary valve 806 may be rotated by thesystem controller to another valve position in which the first andsecond ports 826, 828 for each of the assay channels 821-824 are coveredor sealed by the body side 819. With the assay channel(s) sealed, thebiological sample(s) may undergo an amplification protocol. Forinstance, a thermocycler (not shown) may be positioned adjacent to thethermal-control area 825 and apply thermal energy in accordance with anamplification protocol. In particular embodiments, each of thebiological samples may be positioned within the thermal-control area 825at the same time. In alternative embodiments, the biological samples maybe positioned within the thermal-control area 825 at separate times.

After the biological samples have been amplified, the rotary valve 806may be returned to the corresponding valve positions to load thecorresponding biological sample into the flow channel 842. With thebiological sample disposed within the flow channel 842, the rotary valvemay be rotated to another position in which the flow channel 842 is inflow communication with a reservoir 835. The reservoir 835 may contain,for example, a hydrogenation buffer solution. The biological sample maybe loaded into the reservoir 835. Optionally, the rotary valve 806 andthe pump assembly 818 may be operated in a similar manner to load thebiological samples from the other assay channels into the reservoir 835.The biological samples may then be directed toward another stage. Forexample, the biological samples may flow through the flow channel 842,through the intermediate port 856, and into the intermediate channel810. In alternative embodiments, the biological samples may be directedtoward the rotary valve 808 without first being loaded into thereservoir 835.

As shown in FIG. 23 , the rotary valve 808 includes a flow channel 870and a plurality of reagent reservoirs 871-878. After the biologicalsamples have been prepared using the rotary valve 806, the biologicalsamples may be transported into the reaction chamber 814. Optionally,prior to the biological samples being delivered to the reaction chamber814, the rotary valve 808 may be rotated to fluidically couple one ormore of the reagent reservoirs 871-878 to the reaction chamber 814. Morespecifically, the flow channel 870 may be rotated to a designatedposition to fluidically couple one of the reagent reservoirs 871-878 tothe reaction chamber 814. As such, the rotary valve 808 may be used toprepare the reaction chamber 814 for receiving the biological samples.For example, the reagent reservoirs 871-878 may include clusteringreagents, enzymes, and/or capture probes.

After the biological samples are delivered to the reaction chamber 814,the rotary valve 808 may be selectively rotated to different valvepositions. For example, the rotary valve 808 may be rotated inaccordance with a predetermined cycle to repeatedly deliver reactioncomponents for conducting an SBS protocol. The cycle may be similar tothe cycle shown in Table 1 above. Accordingly, the rotary valve 808 maybe utilized to prepare the reaction chamber for receiving the biologicalsample and/or to conduct an assay protocol.

FIGS. 24 and 25 illustrate another embodiment that utilizes a rotaryvalve having a bridge channel. FIG. 24 is a plan view of a flow-controlsystem 900, and FIG. 25 is a partially exploded perspective view of theflow-control system 900. As shown, the flow-control system 900 includesa microfluidic body 902 having opposite first and second body sides 904,906 (FIG. 25 ). The microfluidic body 902 includes a plurality of flowchannels 908 and a plurality of sample reservoirs 910. Each of the flowchannels 908 is configured to be fluidically coupled to a respectivesample reservoir 910. The flow channels 908 may be similar in shape andsize to the flow channels 536-539 (FIG. 13 ).

The flow-control system 900 also includes a rotary valve 912. The rotaryvalve 912 includes a plurality of bridge channels 913-916 that areconfigured to fluidically couple the corresponding flow channels 908 andsample reservoirs 910. In particular embodiments, each of the bridgechannels 913-916 is an open-sided groove along an exterior of the rotaryvalve 912. In alternative embodiments, the bridge channels 913-916 arenot open-sided and, instead, extend between first and second ports thatopen to the exterior. By way of example, the bridge channel 916 in FIG.24 fluidically couples a corresponding sample reservoir 910 to acorresponding flow channel 908 based on a rotational position of therotary valve 912. As the biological sample flows through the bridgechannel 913, the other bridge channels 914-916 are not fluidicallycoupled to the corresponding sample reservoir 910. More specifically,the other bridge channels 914-916 are sealed by the rotary valve 912.

In a similar manner as described in other embodiments, a thermocycler(not shown) may change a temperature that is experienced by thebiological samples within the flow channels 908. For example, one orboth of the body sides 904, 906 may be engaged by a thermocycler. Afterthe amplification protocol, the biological samples may be delivered toanother spatial region for additional modification/preparation and/oranalysis.

As described above in the various embodiments, the rotary valve and themicrofluidic body may include different fluidic elements that cooperateto control flow of one or more fluids in a designated manner. It is tobe understood that the above embodiments are only illustrative, and notrestrictive. For example, the above-described embodiments (and/oraspects thereof) may be used in combination with each other. Inaddition, many modifications may be made to adapt a particular situationor material to the teachings of the various embodiments withoutdeparting from its scope.

FIGS. 26-29 illustrate various views of a rotary valve 950 formed inaccordance with an embodiment. The rotary valve 950 may be used as therotary valve in various embodiments, such as the rotary valve 216 (FIG.2 ). FIGS. 26 and 27 illustrate a bottom perspective view and a sideperspective view, respectively, of the rotary valve 950. The rotaryvalve 950 includes a fluidic side 952 and an operative side 954. Theoperative side 954 includes a mechanical interface 956 that isconfigured to engage a valve actuator (not shown).

FIG. 28 illustrates a cross-section of the rotary valve 950. As shown,the rotary valve 950 includes a housing cover 960 and a side cover 964that are secured in fixed positions with respect to each other. Thehousing cover 960 defines a valve cavity 962, and the side cover 964closes one end of the valve cavity 962 along the fluidic side 952. Therotary valve 950 also includes a rotor shaft 966 that includes themechanical interface 956, a valve spring 968, a manifold body 970, and acompressible membrane 972 that are each disposed within the valve cavity962. The rotor shaft 966 is configured to rotate the manifold body 970and the compressible membrane 972 alongside the side cover 964 about anaxis 978.

The manifold body 970 is secured to the rotor shaft 966 on one side andsecured to the compressible membrane 972 on an opposite side. The valvespring 968 may bias or urge the manifold body 970 and the compressiblemembrane 972 against an interior surface of the side cover 964. Inparticular embodiments, the compressible membrane 972 may bepolypropylene or other similar material. Returning briefly to FIG. 26 ,the side cover 964 includes a central flow port 980, a drain port 981,and outer flow ports 982. The side cover 964 is partially transparent inFIG. 26 to indicate the central flow port 980, the drain port 981, andthe outer flow ports 982. A total of nine outer flow ports 982 areshown, but other embodiments may include a different number of ports.

FIG. 29 is an enlarged cross-section of the rotary valve 950 thatindicates the interaction between the manifold body 970, thecompressible membrane 972, and the side cover 964. As shown, the sidecover 964 and the compressible membrane 972 may define a lubricationreservoir 990 therebetween. The lubrication reservoir 990 may extendaround the axis 978. In some embodiments, an outer lubrication reservoir991 may also be provided. The lubrication reservoirs 990 are alsoindicated in FIG. 26 . The drain port 981 is in flow communication withthe lubrication reservoir 990 so that a lubricant may be loaded into thereservoir 990. As shown, the manifold body 970 and the compressiblemembrane 972 define a flow channel 984 therebetween. When the rotorshaft 966 rotates the manifold body 970 with the compressible membrane972, the flow channel 984 is rotated therewith. Frictional forces thatresist rotation may be reduced because of the compressible membrane 972and the lubrication reservoir 980. Accordingly, a lifetime operation ofthe rotary valve 950 may be longer than other known valves.

In accordance with an embodiment, a system is provided that includes afluidic network having a sample channel, a reaction chamber, and areservoir. The sample channel is in flow communication with a sampleport that is configured to receive a biological sample. The system alsoincludes a pump assembly that is configured to be in flow communicationwith the fluidic network. The system also includes a rotary valve thathas a flow channel and is configured to rotate between first and secondvalve positions. The flow channel fluidically couples the reactionchamber and the sample channel when the rotary valve is in the firstvalve position and fluidically couples the reservoir and the reactionchamber when the rotary valve is in the second valve position. The pumpassembly induces a flow of the biological sample toward the reactionchamber when the rotary valve is in the first valve position and inducesa flow of a reaction component from the reservoir toward the reactionchamber when the rotary valve is in the second valve position.

In one aspect, the pump assembly may include a system pump that is inflow communication with the reaction chamber and is located downstreamwith respect to the reaction chamber.

In another aspect, the rotary valve may be configured to retain thebiological sample in the flow channel as the rotary valve rotates fromthe first valve position to the second valve position. The pump assemblymay be configured to induce a flow of the biological sample into thereservoir when the rotary valve is in the second valve position.

Optionally, the sample channel may be a first sample channel and thebiological sample may be a first biological sample. The fluidic networkmay include a second sample channel having a second biological sample.The rotary valve may be configured to rotate to a third valve positionsuch that the flow channel is in flow communication with the secondsample channel. The pump assembly may be configured to induce a flow ofthe second biological sample in the second sample channel into the flowchannel, wherein the rotary valve is configured to retain the secondbiological sample in the flow channel as the rotary valve rotates fromthe third valve position to the second valve position. The pump assemblymay be configured to induce a flow of the second biological sampletherein into the reservoir when the rotary valve is in the second valveposition. In some embodiments, the pump assembly may be configured toinduce a flow of the first and second biological samples from thereservoir toward the reaction chamber.

In another aspect, the reservoir may be a first reservoir. The fluidicnetwork further may include a second reservoir, wherein the rotary valvemay be configured to move to a third valve position such that the flowchannel fluidically couples the second reservoir and the reactionchamber.

In another aspect, the sample channel may be a first sample channel andthe fluidic network includes a second sample channel. Optionally, eachof the first and second sample channels may be in flow communicationwith the rotary valve through a common supply port. Optionally, thesystem may also include a channel valve that is coupled to the samplechannel. The channel valve may be configured to move between first andsecond positions to block flow and to permit flow, respectively, throughthe sample channel.

In another aspect, the rotary valve may rotate about an axis. Thefluidic network may include a feed port that is aligned with the axisand fluidically couples the flow channel and the reaction chamber.

In another aspect, the fluidic network may also include a reagentchannel. The sample channel and the reagent channel may be in flowcommunication with a common supply port that is located upstream withrespect to the flow channel. The supply port may fluidically couple thesample channel and the reagent channel to the flow channel.

In another aspect, the system may include a detection assembly that isconfigured to detect designated reactions within the reaction chamber.Optionally, the detection assembly includes an imaging detector that maybe positioned to detect light signals from the reaction chamber.Optionally, the imaging detector may have a fixed location with respectto the fluidic network.

In another aspect, the system includes a system controller that may beconfigured to automatically control the rotary valve and the pumpassembly to conduct iterative cycles of a sequencing-by-synthesis (SBS)protocol.

In an embodiment, a method is provided that includes rotating a rotaryvalve having a flow channel to a first valve position. The flow channelis in flow communication with a reaction chamber when in the first valveposition. The method may also include flowing a biological sample from asample channel or a first reservoir through the flow channel and intothe reaction chamber when the rotary valve is in the first valveposition. The method may also include rotating the rotary valve to asecond valve position. The flow channel may fluidically couple a secondreservoir and the reaction chamber when in the second valve position.The method may also include flowing a reaction component from the secondreservoir into the reaction chamber. The reaction component interactswith the biological sample within the reaction chamber.

In one aspect, the method may include detecting designated reactionsbetween the reaction component and the biological sample within thereaction chamber. Optionally, detecting the designated reactions mayinclude detecting light signals from the reaction chamber. The lightsignals may be indicative of the designated reactions.

In another aspect, the method also includes separately flowing aplurality of the biological samples into the reservoir thereby combiningthe biological samples therein. The biological samples maysimultaneously flow through the flow channel and into the reactionchamber when the rotary valve is in the first valve position.

In another aspect, the method also includes rotating the rotary valve toa third valve position and flowing a wash solution from the thirdreservoir into the reaction chamber. The method may also includerotating the rotary valve to the second valve position and flowing thereaction component from the second reservoir into the reaction chamber.Optionally, the method includes executing iterative cycles of asequencing-by-synthesis (SBS) protocol.

In another aspect, the method also includes amplifying the biologicalsample within the sample channel or the reservoir prior to flowing thebiological sample through the flow channel and into the reactionchamber.

In an embodiment, a system is provided that includes a flow-controlsystem having a fluidic network and a pump assembly that is in flowcommunication with the fluidic network. The fluidic network includes asample channel that is configured to receive a biological sample, aplurality of reservoirs, and a reaction chamber. The system alsoincludes a rotary valve having a flow channel. The rotary valve isconfigured to rotate to different valve positions to fluidically couplethe reaction chamber to the sample channel or to one of the reservoirs.The system also includes a detection device that is configured to detectlight signals from the reaction chamber during an assay protocol. Thesystem also includes a system controller that is configured to controlthe rotary valve and the pump assembly to flow the biological samplefrom the sample channel and into the reaction chamber. The systemcontroller is also configured to control the rotary valve, the pumpassembly, and the detection device during a plurality of protocolcycles, wherein each of the protocol cycles includes: (a) rotating therotary valve to a first reservoir-valve position such that the reactionchamber is in flow communication with a first reservoir of the pluralityof reservoirs; (b) controlling the pump assembly to induce a flow of afluid from the first reservoir into the reaction chamber; (c) rotatingthe rotary valve to a second reservoir-valve position such that thereaction chamber is in flow communication with a second reservoir of theplurality of reservoirs; (d) controlling the pump assembly to induce aflow of a fluid from the second reservoir into the reaction chamber; and(e) controlling the detection device to detect the light signals fromthe reaction chamber while the fluid from the second reservoir flowsthrough the reaction chamber or after the fluid from the secondreservoir flows through the reaction chamber.

In one aspect, the sample channel may include a sample-preparationregion. The system may also include a thermocycler that is configured tocontrol a temperature of the biological sample within thesample-preparation region. The system controller may control thethermocycler to amplify the biological sample within thesample-preparation region prior to flowing the biological sample fromthe sample channel into the reaction chamber.

Optionally, each of the protocol cycles includes rotating the rotaryvalve to a third reservoir-valve position such that the reaction chamberis in flow communication with a third reservoir of the plurality ofreservoirs and controlling the pump assembly to induce a flow of a fluidfrom the third reservoir into the reaction chamber.

In another aspect, the detection device includes a CMOS imagingdetector. In another aspect, a flow cell is coupled to the detectiondevice. The flow cell may define the reaction chamber. Optionally, theflow cell is secured in a fixed position with respect to the detectiondevice.

In another aspect, the flow-control system includes a microfluidic bodyhaving a body side. The body side may include a plurality of ports thatopen to the body side, wherein the rotary valve seals a plurality of theports when the flow channel is fluidically coupled to at least one ofthe other ports. In particular embodiments, the system is configured toexecute a sequencing-by-synthesis (SBS) protocol.

In accordance with an embodiment, a method is provided that includesproviding a microfluidic body and a rotary valve. The microfluidic bodyhas a body side and a fluidic network that includes a supply port and afeed port. The supply port opens to the body side. The rotary valve isrotatably mounted to the body side. The rotary valve has a first channelport, a second channel port, and a flow channel that extends between thefirst channel port and the second channel port. The method also includesrotating the rotary valve to a first valve position at which the firstchannel port is in flow communication with the supply port of themicrofluidic body. The method also includes flowing a biological samplethrough the first channel port and into the flow channel when the rotaryvalve is in the first valve position. The method also includes rotatingthe rotary valve to a second valve position with the biological samplewithin the flow channel such that the first channel port is sealed bythe body side. The method also includes performing a thermocyclingoperation to change a temperature of the biological sample in the flowchannel to a select temperature.

In one aspect, the microfluidic body may include a reservoir port thatopens to the body side and is in flow communication with a reservoir Themethod may also include rotating the rotary valve to align the firstchannel port and the reservoir port and inducing a flow of thebiological sample within the flow channel through the first channel portinto the reservoir. Optionally, the method includes inducing a flow ofthe biological sample from the reservoir through the flow channel andthrough the feed port of the microfluidic body.

In another aspect, the second channel port may be aligned with the feedport when the rotary valve is in the second valve position.

In another aspect, the second channel port may be sealed by the bodyside when the rotary valve is in the second valve position.

In another aspect, the first channel port is a first inlet port and theflow channel is a first flow channel. The rotary valve may include asecond inlet port and a second flow channel. The second flow channel mayextend between the second inlet port and the second channel port.

In another aspect, the first channel port is a first inlet port and thesecond channel port is a first outlet port. The rotary valve may includea second inlet port and a second outlet port with a flow channelextending therebetween.

In another aspect, the rotary valve may include a fluidic side and anoperative side that face in opposite directions. The thermocycler mayengage the operative side to control the temperature of the biologicalsample.

In another aspect, the method may include inducing a flow of thebiological sample from the reservoir through the flow channel andthrough the feed port of the microfluidic body into a reaction chamber.The method may also include detecting light signals from the reactionchamber. Optionally, the reaction chamber has a remote location withrespect to the rotary valve.

In another aspect, a flow cell includes the reaction chamber. Detectingthe light signals from the reaction chamber may include detecting thelight signals using an imaging detector that is coupled to the flowcell. Optionally, the imaging detector and the flow cell are secured toeach other.

In accordance with an embodiment, a system is provided that includes amicrofluidic body having a body side and a fluidic network that includesa supply port and a feed port. The supply port opens to the body side.The system also includes a rotary valve that is rotatably mounted to thebody side. The rotary valve has a first channel port, a second channelport, and a flow channel that extends between the first and secondchannel ports. The rotary valve is configured to rotate between firstand second valve positions. The first channel port is in flowcommunication with the supply port of the microfluidic body when therotary valve is in the first valve position. The first channel port issealed by the microfluidic body when the rotary valve is in the secondvalve position. The system also includes a pump assembly that isconfigured to induce a flow of a fluid through the supply port and intothe flow channel when the rotary valve is in the first valve position.The system also includes a thermocycler that is positioned relative tothe rotary valve and configured to control a temperature experienced bythe fluid within the flow channel when the rotary valve is in the secondvalve position.

In one aspect, the microfluidic body may include a reservoir port thatopens to the body side and is in flow communication with a reservoir.The rotary valve may be rotatable to a third valve position in which thefirst channel port and the reservoir port are aligned. The pump assemblymay be configured to induce a flow of the fluid in the flow channelthrough the reservoir port and into the reservoir. Optionally, the pumpassembly is configured to induce a flow of the fluid from the reservoirthrough the flow channel and through the feed port of the microfluidicbody.

In another aspect, the rotary valve is configured to rotate about anaxis. The second channel port and the feed port may be aligned with theaxis.

In another aspect, the flow channel may be a first flow channel. Therotary valve may include a second flow channel that extends betweencorresponding channel ports.

In another aspect, the system includes a reaction chamber in flowcommunication with the feed port and a detection device that ispositioned to detect designated reactions within the reaction chamber.Optionally, the reaction chamber has a remote location with respect tothe rotary valve. Optionally, the system includes a flow cell having thereaction chamber. The detection device may be an imaging detector thatis positioned adjacent to the flow cell. In some embodiments, theimaging detector and the flow cell may be secured to each other.

In accordance with an embodiment, a system is provided that includes amicrofluidic body having a fluidic network that has an inlet port, anoutlet port, and a sample reservoir. The system also includes a rotaryvalve that is rotatably coupled to the microfluidic body. The rotaryvalve has a first channel segment and a second channel segment. Thefirst channel segment fluidically couples the inlet port and the samplereservoir when the rotary valve is in a first valve position. The secondchannel segment fluidically couples the outlet port and the samplereservoir when the rotary valve is in the first valve position. Thesystem also includes a pump assembly configured to flow a fluid throughthe inlet port and the first channel segment into the sample reservoirwhen the rotary valve is in the first valve position. The rotary valveis configured to move to a second valve position in which the samplereservoir is sealed by the rotary valve. The system may also include athermocycler that is positioned relative to the microfluidic body toprovide thermal energy to the sample reservoir when the rotary valve isin the second valve position.

In one aspect, the rotary valve may include an enclosed gas reservoir.The enclosed gas reservoir may be aligned with the sample reservoir whenthe rotary valve is in the second valve position. The enclosed gasreservoir and the sample reservoir may combine to form a reactionchamber.

In another aspect, the system also includes a feed channel that is inflow communication with the outlet port. The feed channel mayfluidically couple the outlet port to a reaction chamber. The systemincludes the reaction chamber and a detection device that is positionedto detect designated reactions within the reaction chamber.

In another aspect, the reaction chamber may have a remote location withrespect to the rotary valve. Optionally, the system may include a flowcell having the reaction chamber. The detection device may be an imagingdetector that is positioned adjacent to the flow cell.

In accordance with an embodiment, a system is provided that includes amicrofluidic body having a fluidic network that has a sample reservoirand a separate assay channel. The assay channel extends between firstand second ports. The fluidic network also includes a feed port. Thesystem may also include a thermocycler that is positioned adjacent to athermal-control area of the microfluidic body. The assay channel extendsthrough the thermal-control area. The thermocycler is configured toprovide thermal energy to the thermal-control area. The system alsoincludes a rotary valve that is rotatably coupled to the microfluidicbody and configured to move between first and second valve positions.The rotary valve has a bridge channel and a separate flow channel. Thebridge channel fluidically couples the sample reservoir and the firstport of the assay channel and the flow channel fluidically couples thesecond port of the assay channel and the feed port when the rotary valveis in the first valve position. The rotary valve is configured to moveto a second valve position to seal the first and second ports of theassay channel.

In one aspect, the flow channel may be configured to receive abiological sample from the assay channel. The rotary valve may beconfigured to rotate to a third valve position in which the flow channelis fluidically coupled to a reservoir. The biological sample may bepermitted to flow through the flow channel into the reservoir.

In another aspect, the system includes a reaction chamber that is inflow communication with the feed port and a detection device that ispositioned to detect designated reactions within the reaction chamber.Optionally, the reaction chamber may have a remote location with respectto the rotary valve. Optionally, the system also includes a flow cellhaving the reaction chamber. The detection device may be an imagingdetector that is positioned adjacent to the flow cell.

As used herein, an element or step recited in the singular and proceededwith the word “a” or “an” should be understood as not excluding pluralof said elements or steps, unless such exclusion is explicitly stated.Furthermore, references to “one embodiment” are not intended to beinterpreted as excluding the existence of additional embodiments thatalso incorporate the recited features. Moreover, unless explicitlystated to the contrary, embodiments “comprising” or “having” an elementor a plurality of elements having a particular property may includeadditional elements whether or not they have that property.

It should be noted that the particular arrangement of components (e.g.,the number, types, placement, or the like) of the illustratedembodiments may be modified in various alternate embodiments. In variousembodiments, different numbers of a given module or unit may beemployed, a different type or types of a given module or unit may beemployed, a given module or unit may be added, or a given module or unitmay be omitted.

It is to be understood that the above description is intended to beillustrative, and not restrictive. For example, the above-describedembodiments (and/or aspects thereof) may be used in combination witheach other. In addition, many modifications may be made to adapt aparticular situation or material to the teachings of the variousembodiments without departing from its scope. Dimensions, types ofmaterials, orientations of the various components, and the number andpositions of the various components described herein are intended todefine parameters of certain embodiments, and are by no means limitingand are merely exemplary embodiments. Many other embodiments andmodifications within the spirit and scope of the claims will be apparentto those of skill in the art upon reviewing the above description. Thepatentable scope should, therefore, be determined with reference to theappended claims, along with the full scope of equivalents to which suchclaims are entitled.

As used in the description, the phrase “in an exemplary embodiment” andthe like means that the described embodiment is just one example. Thephrase is not intended to limit the inventive subject matter to thatembodiment. Other embodiments of the inventive subject matter may notinclude the recited feature or structure. In the appended claims, theterms “including” and “in which” are used as the plain-Englishequivalents of the respective terms “comprising” and “wherein.”Moreover, in the following claims, the terms “first,” “second,” and“third,” etc. are used merely as labels, and are not intended to imposenumerical requirements on their objects. Further, the limitations of thefollowing claims are not written in means—plus-function format and arenot intended to be interpreted based on 35 U.S.C. § 112(f), unless anduntil such claim limitations expressly use the phrase “means for”followed by a statement of function void of further structure.

1. A system comprising: a microfluidic body having a body side and afluidic network that includes a supply port and a feed port, the supplyport opening to the body side; a rotary valve that is rotatably mountedto the body side, the rotary valve having a first channel port, a secondchannel port, and a flow channel that extends between the first andsecond channel ports, the rotary valve configured to rotate betweenfirst and second valve positions, the first channel port being in flowcommunication with the supply port of the microfluidic body when therotary valve is in the first valve position, the first channel portbeing sealed by the microfluidic body when the rotary valve is in thesecond valve position; and a pump assembly configured to induce a flowof a fluid through the supply port and into the flow channel when therotary valve is in the first valve position; and a thermocyclerpositioned relative to the rotary valve and controls a temperatureexperienced by the fluid within the flow channel when the rotary valveis in the second valve position.
 2. The system of claim 1, wherein themicrofluidic body includes a reservoir port that opens to the body sideand is in flow communication with a reservoir, the rotary valve beingrotatable to a third valve position in which the first channel port andthe reservoir port are aligned, the pump assembly configured to induce aflow of the fluid in the flow channel through the reservoir port andinto the reservoir.
 3. The system of claim 2, wherein the pump assemblyis configured to induce a flow of the fluid from the reservoir throughthe flow channel and through the feed port of the microfluidic body. 4.The system of claim 1, wherein the rotary valve is configured to rotateabout an axis, the second channel port and the feed port being alignedwith the axis.
 5. The system of claim 1, wherein the flow channel is afirst flow channel, the rotary valve including a second flow channelextending between corresponding channel ports.
 6. The system of claim 1,further comprising a reaction chamber in flow communication with thefeed port and a detection device that is positioned to detect designatedreactions within the reaction chamber.
 7. The system of claim 6, whereinthe reaction chamber has a remote location with respect to the rotaryvalve.
 8. The system of claim 6, wherein a flow cell includes thereaction chamber, the detection device being an imaging detector that ispositioned adjacent to the flow cell.
 9. The system of claim 8, whereinthe imaging detector and the flow cell are secured to each other.
 10. Asystem comprising: a microfluidic body having a fluidic network thatincludes an inlet port, an outlet port, and a sample reservoir; a rotaryvalve that is rotatably coupled to the microfluidic body, the rotaryvalve having a first channel segment and a second channel segment,wherein the first channel segment fluidically couples the inlet port andthe sample reservoir when the rotary valve is in a first valve positionand the second channel segment fluidically couples the outlet port andthe sample reservoir when the rotary valve is in the first valveposition; a pump assembly configured to flow a fluid through the inletport and the first channel segment into the sample reservoir when therotary valve is in the first valve position, wherein the rotary valve isconfigured to move to a second valve position in which the samplereservoir is sealed by the rotary valve; and a thermocycler positionedrelative to the microfluidic body to provide thermal energy to thesample reservoir when the rotary valve is in the second valve position.11. The system of claim 10, wherein the rotary valve includes anenclosed gas reservoir, the enclosed gas reservoir being aligned withthe sample reservoir when the rotary valve is in the second valveposition, the enclosed gas reservoir and the sample reservoir combiningto form a reaction chamber.
 12. The system of claim 10, furthercomprising a feed channel in flow communication with the outlet port,the feed channel fluidically coupling the outlet port to a reactionchamber, wherein the system includes the reaction chamber and adetection device that is positioned to detect designated reactionswithin the reaction chamber.
 13. The system of claim 12, wherein thereaction chamber has a remote location with respect to the rotary valve.14. The system of claim 12, wherein a flow cell includes the reactionchamber, the detection device being an imaging detector that ispositioned adjacent to the flow cell.
 15. A system comprising: amicrofluidic body having a fluidic network that includes a samplereservoir and a separate assay channel, the assay channel extendingbetween first and second ports, the fluidic network also including afeed port; a thermocycler positioned adjacent to a thermal-control areaof the microfluidic body, the assay channel extending through thethermal-control area, the thermocycler configured to provide thermalenergy to the thermal-control area; and a rotary valve that is rotatablycoupled to the microfluidic body and configured to move between firstand second valve positions, the rotary valve having a bridge channel anda separate flow channel, the bridge channel fluidically coupling thesample reservoir and the first port of the assay channel and the flowchannel fluidically coupling the second port of the assay channel andthe feed port when the rotary valve is in the first valve position,wherein the rotary valve is configured to move to a second valveposition to seal the first and second ports of the assay channel. 16.The system of claim 15, wherein the flow channel is configured toreceive a biological sample from the assay channel, the rotary valveconfigured to rotate to a third valve position in which the flow channelis fluidically coupled to a reservoir, the biological sample permittedto flow through the flow channel into the reservoir.
 17. The system ofclaim 15, further comprising a reaction chamber in flow communicationwith the feed port and a detection device that is positioned to detectdesignated reactions within the reaction chamber.
 18. The system ofclaim 17, wherein the reaction chamber has a remote location withrespect to the rotary valve.
 19. The system of claim 17, wherein a flowcell includes the reaction chamber, the detection device being animaging detector that is positioned adjacent to the flow cell.
 20. Thesystem of claim 19, wherein the imaging detector and the flow cell aresecured to each other. 21-34. (canceled)